Allied intelligence suggested that the beachheads contained about 4,000 Japanese troops, mostly tattered survivors of the fighting in the Owen Stanley Range. Remnants of the 41st Regiment had indeed reached Buna, after the 144th Regiment attempted to block the Australian advance at Oivi-Gorari, but thousands of other army and naval troops had been sent to Buna to construct the forward base and to help defend. Ships had evacuated most of the badly wounded and sick men who managed to reach Buna from the mountains, and the men who remained - up to 9,000 of them - were determined to fight tenaciously and, with nowhere to retreat, even to the death.

In the four months after first landing at Gona, Japanese engineers had constructed hundreds of bunkers around the beachheads' perimeter using coconut palm logs and compacted earth that could withstand small arms fire and some artillery shelling. The bunkers, many of them housing heavy machine-guns, were camouflaged naturally by fast growing vegetation, which hid them from aerial reconnaissance.

Australian soldiers examine a destroyed Japanese machine gun nest, Buna, 28 December 1942

On 14 November 1942, General MacArthur ordered the Allied forces to finish the Papuan campaign by capturing the beachheads. The Australians of Maroubra Force, who had fought across the Owen Stanley Range, were weary, with units down to one-third of normal strength. Nevertheless, they were ordered to attack and capture Sanananda and Gona, without reinforcements, although a battalion of American troops who had crossed the Jaure Trail unopposed assisted with the first attacks on the Sanananda Track. Two regiments of the American 32nd Division, which had advanced along the coast unopposed, would attack Buna.

On 16 November, three days before the Allies were to attack, the Japanese inflicted the first serious blow. A convoy of American small ships carrying artillery and supplies was detected by fighter-bombers and all five vessels were destroyed. More were sunk over the following days or ran aground on reefs or sandbars.

On 19 November, the American 128th Regiment attacked Buna and nearby Cape Endaiadere. The "green" troops were confident as they advanced through swamp and jungle but were ambushed and suffered many casualties. The Australians also came up against bunkers but delayed their opening attacks because the men were exhausted after trekking across the hot coastal plain and were short of supplies. Both the 25th Brigade, attacking Gona, and the 16th Brigade, advancing up the central Sanananda Track, attacked next day after transport aircraft dropped supplies. Dozens of men were killed or wounded for little progress.

New Guinea Force had planned to supply the attacking forces using small ships and aircraft but, after the small ships were attacked, demand for air supply soared. By 21 November, two airfields were opened behind the fronts and an "air bridge" was established to fly bulk supplies, equipment and men in from Port Moresby. The American air commander, Lieutenant General George C. Kenney, ordered a fighter "umbrella" over the beachheads so that transport aircraft were protected while flying to and from the forward area and on the ground. One of the great disadvantages for the Japanese garrison was that they did not have a similar means of resupply and reinforcement.

Inside the beachheads, Japanese troops were suffering a malaria epidemic. The "wet season" had swelled swamps and medical supplies were running low. The remaining troops were determined to hold ground and had stockpiles of ammunition, but they could not combat the dreaded anopheles mosquito. They were also short on food. An 18th Army staff officer who arrived to check on the situation was appalled to encounter some sick and emaciated men begging for any food, medicine or cigarettes he could spare.

Japanese fighter-bombers based at Lae and Salamaua continued to patrol over the area, sometimes bombing and strafing Allied positions. The Americans had an early warning system to keep transport aircraft away while enemy fighters were present and the American fighters, mostly twin-engine Lockheed P-38 Lightning, were more than a match for the Mitsubishi A6M ('Zero') and Nakajima Ki-43 Hayabusa ('Oscar') fighters. The Allies established control of the skies over Buna.

By 25 November, it was obvious that fierce Japanese resistance had stalled the Allied attacks. Australian artillery was brought in by air and sea, but troops lacked the energy and, in some cases, determination to push on. Self-inflicted wounds were encountered amongst American casualties. Tropical diseases also emerged as a serious problem for the Allies who, like the Japanese, suffered a malaria epidemic. Although Allied scientists and medical officers had warned of the threat, troops did not have enough anti-malarial drugs and did not know the best anti-malarial measures, like wearing long-sleeved shirts and trousers. It was also hard for both sides to control the disease in a battle area because shell holes filled with water (an ideal home for mosquito larvae) and troops in the front-line could not sleep under mosquito nets in case of an enemy attack.

The Allies had an advantage in being able to call in reinforcements. New Guinea Force arranged for the Australian 21st and 30th Brigades, which had served on the Kokoda Track early in the campaign, to relieve the exhausted 16th and 25th Brigades. Later, the 18th Brigade was brought from Milne Bay to take over from the Americans attacking Buna.

Soldiers of the Australian 2/7th Cavalry Regiment in their foxholes with weapons at the ready, Sanananda, January 1943.

Despite mounting casualties, Japanese troops continued to defend each bunker tenaciously, giving ground only after inflicting heavy losses on attacking troops. The Allies found that close air support was ineffective because it was too hard for pilots to spot targets and bomb and strafe accurately, and artillery did not give a clear edge. On 9 December, the 21st Brigade captured Gona, with artillery support, but the casualty rate among attacking troops was too heavy to sustain. New Guinea Force hoped to break the deadlock by deploying light tanks.

The first attack using tanks was effective but, once the element of surprise was lost, they began suffering high casualties as Japanese gunners began targeting the three or four tanks used in each action. Nevertheless, by 3 January 1943 the last positions around Buna had fallen to the 18th Brigade. Only fifty Japanese survived this action, most becoming prisoners of war.

The final strongpoint to hold out was Sanananda. The Japanese had skilfully located bunkers and machine-gun posts on the only dry land in the area, so the Australians and Americans in this sector had to advance through, and live in, swamp. Though now disorganised and in poor condition, the Japanese continued to resist every Allied attack. Australian troops of the 30th Brigade, poorly trained for battle, suffered over 50 per cent losses in their opening attacks. The 18th Brigade was brought over from Buna and made some progress, but again the battle came to a standstill.

On 12 January 1943 , the 18th Army's commander, General Adachi, ordered the evacuation of Sanananda. About 2,000 troops escaped by sea or on foot by the end of the battle. The Allies had nearly given up hope when it became clear that most of the Japanese had left. On 22 January, the 18th Brigade finished mopping-up actions and the Papuan campaign officially came to an end the following day.