Waseem and Shahnawaz were caught by a police team from Charthawal Road after a brief exchange of fire last night, SSP Deepak Kumar said.
He said Waseem was injured in the shootout.
The duo and five others shot dead three people and injured three on August 4 at Daroga Kothi, he said.
Three persons were shot dead and as many injured over a monetary dispute on August 4. Tension had prevailed in the area after the incident.
A cash reward of Rs 5000 has been announced for the police team.