Barnsley were hard done by - having at least deserved a point - but their inability to convert other chances when 1-0 up proved costly and they slumped to their second successive home defeat.
Paul Hart's men included striker Michael Chopra signed on loan from Newcastle and making his debut alongside target man Barry Conlon.
But it was Hull's own big centre forward, Aaron Wilbraham, who had the best of the early chances when he was presented with a clear header eight yards out which he failed to get on target.
Barnsley got their noses in front in the 13th minute with another well worked set piece move. Chris Shuker delivered a corner into the six yard box and Conlon was unmarked to head in for his second goal in as many games.
Hull almost replied a minute later, Wilbraham again being given a good opportunity but he dragged his shot wide from 12 yards.
There were other chances as the half wore on and Wibraham was only denied an equaliser by a brilliant block from Barnsley captain Tony Vaughan.
The home side started the second period in positive fashion and both Chopra and Paul Reid went close, before Conlon spurned a great chance from 12 yards.
Barnsley were made to pay as Hull levelled on 58 minutes, Stuart Elliott rising highest in a crowded box to head home an Andy Dawson corner.
Barnsley sent on another on-loan striker in Manchester United youngster Daniel Nardiello and he immediately linked up well with Chopra but sent an angled shot agonisingly wide of the far post.
And it was Hull who completed their smash and grab raid when Keane popped up to deliver the knock out blow with his quality finish.