Eleven suicide attackers on Tuesday breached the high-security complex which also houses a joint NATO-Afghan base, taking families hostage and triggering pitched firefights with soldiers.
The raid, which saw militants blowing themselves up among civilians before the area was secured, is the most serious attack in 14 years of war on the complex, the largest military installation in the south of the country.
"Fifty of our innocent countrymen, including 10 soldiers, two policemen and 38 civilians, were martyred in the attack," the defence ministry said in a statement.
"A group of 11 terrorists attacked a bazaar and a school in the airport complex, took up positions in the area and (some of them) detonated their suicide vests among civilians."
Witnesses said the militants had taken families hostage, using them as "human shields" and slowing down the military's clearance operation.
Some 27 hours after the siege began, soldiers late Wednesday killed the last insurgent who was holed up inside a building and doggedly resisted security forces till the very end.
The Taliban posted a picture on their website of the militants it said were involved in the attack. It shows 10 young men sporting trimmed beards, Kalashnikovs and identical military uniforms.
"This is the most serious attack we've witnessed against the largest military installation in southern Afghanistan," a Western official told AFP.
"But it seems that the insurgents failed to get inside the base itself, so it's not a security breach on the scale of the Camp Bastion attack in 2012."
In September 2012, Taliban militants, armed with suicide vests, guns and rockets, and wearing US uniforms, breached the outer wall of Camp Bastion, a heavily fortified airfield in southern Helmand province.
Two US marines were killed and millions of dollars' worth of aircraft were destroyed in the unprecedented attack before the entire raiding force was killed or captured.