The air base is located near the border with Pakistan.
"The gunbattle between terrorists and security forces ended after more than five hours," Punjab Police ADGP (Law and Order) H S Dhillon.
"However, the area was not sanitised yet and the combing operation continues," he said.
At least four to five militants, believed to be from the Jaish-e-Mohammed terrorist group, in army uniform launched the attack at 3:30 AM with an aim of destroying the air base, a top security official said.
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The terrorists, with huge quantity of RDX in their possession, made their way to the base from the back side where there is a jungle, they said.
Authorities said helicopters and other equipment at the Air base are safe. The technical area of the Air Force station is safe, police said, adding the entire area has been cordoned off.
Pathankot SSP R K Bakshi said four suspected militants were killed in the battle.Two jawans were also martyred and six sustained injuries.
The attackers were met with strong resistance from the security personnel, who were already alert to the possibility of an attack, top sources said in Delhi, adding that the terrorists, therefore, could not enter the air base and managed to reach only to the langer area on the outside.
Sources said that a co-ordinated counter operation supervised by NSA Ajit Doval was launched to neutralise the terrorists.
Security establishment was already on alert and anticipating an attack after an SP of Punjab Police was abducted by a group of men in army uniform on Thursday night.