This is Sen's maiden entry in the final of a BWF World Tour Super 500 event.
Sen, the third seed in the USD 400,000 event, lost a close first game 19-21 in the semi-final but came back strongly to win the next two games 21-16, 21-12 to emerge victorious in just over one hour at the KD Jadhav Indoor Hall here.
In the first game, Sen, who won a bronze medal in the BWF World Championships in December, came back from 1-4 down to level scores at 4-4 before he opened up a small lead at 10-7.
It was an up-and-down affair as Yong fought back to level scores at 14-14 and though Sen again caught up with his rival at 17-all, the Malaysian capitalised on some errors by the Indian shuttler and won the first game.
The second game was a close affair initially as the lead changed hands repeatedly before Sen took control of the proceedings after 12-12 and went on to win the game at 21-16.
In the decider, the Indian took an early lead and cruised to victory, always maintaining his upper hand as his Canadian rival wilted under pressure.
"The first game was pretty close and I made a few errors and that cost me the first game. But I managed to keep my calm and managed to pull off (a win)," Sen said in the post-match comments provided by the organisers.
In the final, Sen will meet reigning World Champion Loh Kean Yew of Singapore, who progressed when his opponent Brian Yang of Canada pulled out complaining of sore throat and headache. Yang had tested negative in the mandatory Covid test but still decided to withdraw from the event.
Yang's withdrawal came soon after two players, a Russian mixed doubles pair, had to pull out in the morning when one of them tested positive for Covid-19. The player returned a positive result to a mandatory RT-PCR test conducted on Friday.
Asked about his upcoming encounter with Loh Kean Yew in the final, Lakshya Sen said it will be a good match as both are playing well.
"I think both of us are playing well and it would be a good match tomorrow and I am looking forward to playing him.
"It's a good feeling to play in my home country and though there were not a lot of supporters in the hall, there were a few who were supporting me and it felt good," Sen said after his victory in the semi-final.
This will be the fifth encounter between Sen and Loh Kean. Both are tied 2-2 in head-to-head.