There had been a promising start from Blues with Walter Pandiani in particular an early danger with a powerful shot against the post and a close-range header.
Jermaine Pennant had created both chances but the youngster, who joined Blues from Arsenal midweek, strived manfully to plot Blackburn's downfall in a hectic first half but with little success.
He provided a non-stop service from the right but no-one was on hand to take advantage of his quality play, as was indicated when Pandiani failed again to score from close range.
New Zealander Ryan Nelsen, who has made such an impressive start to his Premiership career, was again the cornerstone of Blackburn's impressive away performance.
He rarely ventured far from his central defensive role and consequently Blues experienced problems breaking down the opposition despite the tantalising play of Pennant.
It was not until the 60th minute that Blues finally broke down Blackburn's resistance when Robbie Blake grabbed the equaliser within a minute of replacing Mehdi Nafti.
The goal sparked off a blistering finish and with Heskey suddenly finding some determined form and the England striker snatched the superb 80th minute winner.
The ball ran loose into the path of Heskey who rammed his shot into the back of the net with the kind of lethal finishing which made him a star in the early part of his career.
Man of the Match: Jermaine Pennant - Maintained his impressive form for Birmingham since his arrival from Arsenal and showed that a £3million fee could prove to be a bargain.