The match's first effort came through Billy Sharp, whose free kick was deflected narrowly over the crossbar.
Wednesday hit back with an effort of their own shortly after, as some good work down the left and a cross into the box from Jeremy Helan left Leon Best with a great chance just a few yards from goal, but he failed to convert.
The miss would prove costly as with 32 minutes played, Chris Brown tapped home from virtually on the line after the returning Chris Kirkland could only parry Sharp's initial effort.
Chris Maguire came close to levelling the contest with just under an hour played by shooting on the turn, only for his effort to be kept out by a one-handed save from Sam Johnstone.
Doncaster looked to further extend their lead through David Cotterill, whose strike from a free kick was well kept out by Kirkland.
Wednesday struggled to create any real opportunities in the closing stages and Doncaster held out for the three points to maintain their unbeaten streak.