Bindra scored 205.3 to win the gold, while Baki scored 202.1.
Daniel Rivers of England settled for bronze at the Barry Buddon Shooting Centre on Friday.
The 3.2 points deficiency meant Baki let a chance to end Bangladesh's 12-year wait of winning a gold medal in the games slip away.
The 20th version of the games kicked off at the Celtic Park on Wednesday.
Altogether 4500 athletes from 71 nations are fighting it out in the competition.
