Indian police said on Sunday that the two were members of the outlawed Jaish-e-Muhammad.
They claimed to have gunned down the pair while they waited for an arms consignment.
The killings came hours after police recovered huge quantities of explosives from New Delhi's railway station.
Earlier in the day, Indian security forces also claimed to have killed another high ranking Jaish-e-Mohammad member in Indian administered Kashmir.
The New Delhi shootout took place just before midnight near a park, a police spokesman said.
The two men were said to be waiting to pick up a delivery of arms and opened fire when police approached them.
Police had learnt about the pick-up from three men arrested several hours earlier after a fruit truck was intercepted carrying hand grenades, shells and a grenade launcher.
"These three men were supposed to deliver the consignment to the two militants," the police spokesman said, adding that an Ak-56 rifle, bullets and two loaded pistols were recovered from the killed men.
A Pakistan-based group that aims to liberate Kashmir from Indian rule, Jaish-e-Mohammad is accused by New Delhi of the attack on the Indian Parliament on 13 December 2001.
The Indian capital and other major cities have been on high alert since two car-bomb explosions killed 52 people in Mumbai on Monday last.
India accuses Pakistan of arming and training those behind the attacks, a charge that Islamabad strongly denies.
Pakistan says it only extends moral support to the Kashmiri fighters, who are seeking to end Indian rule in the disputed territory.