The attack comes within days of Prime Minister Narendra Modi's unscheduled stopover in Lahore while returning from Russia via Afghanistan.
Modi condemned the attack and said that enemies of humanity who could not see the nation succeed had attempted to cause harm to the armed forces.
"The nation stands united against these enemies and their evil designs will never succeed. I am proud of the jawans and security forces martyred during the operation," Modi said at a public function in Mysuru, about 140km from Bengaluru.
"Proud of our Jawans and security forces," a tweet from PMO India earlier quoted Modi as saying.
Despite criticism from some Congress leaders of the government's policy towards Pakistan, home minister Rajnath Singh only said the government wants peace and good relations with all its neighbours, including Pakistan, but would not shy from giving a befitting reply.
"Let them (opposition) say whatever they like, but our policy is clear. We want peace. But we will not tolerate any terrorist activity on our soil and will give a befitting response," Singh said.
Unidentified terrorists attacked the IAF base in Punjab's Pathankot town early on Saturday, leaving three IAF personnel and five terrorists dead.
Rajnath Singh's cabinet colleague Prakash Javadekar, while supporting his stance of giving a "befitting reply" to terror", did not rule out talks with Pakistan in future.
"As far as Pakistan is concerned, it is our neighbour. Talks will take place keeping terror as the key issue," he said, adding that "Prime Minister Narendra Modi has made a beginning, now it is Pakistan's turn to reciprocate.
Meanwhile, Pakistan has condemned the Pathankot attack.