Pathan recorded career-best T20 figures of 5/13 in four overs as Assam were restricted to 116 for 9 in 20 overs reply to Baroda's decent score of 165 for eight.
The left-arm seamer, who is leading Baroda finished his spell with the new ball in one stretch getting wickets in all his four overs.
Irfan, who would like to keep both IPL franchises as well as national selectors interested, bowled sharply as got the ball to move away consistently and few that straightened after pitching.
Left-hander Pallav Kumar Das (1) got one that came in while right-handers Sarupam Purakayashtha (4) and KB Arun Karthik (9) got away going deliveries.
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Earlier, when Baroda batted, Kedar Devdhar and Deepak Hooda contributed 48 runs each in Baroda's total. Yusuf Pathan scored 9 but the biggest flop show was Hardik Pandya, who managed only five runs and also gave away 27 from 3 overs.
Assam 116/9 in 20 overs (Irfan Pathan 5/13, Swapnil Singh 2/15). Baroda won by 49 runs.