Rovers dominated possession throughout as they played the game at a high tempo and quickly closed their opponents down when they had the ball.
Big striker Mark McCammon, recalled to the starting line-up after a lengthy absence, put Rovers on the path to victory with a well-taken goal in the 11th minute.
The Doncaster build-up was excellent and Northampton were caught out at the back when James Coppinger crossed from the right and McCammon was left unmarked at the far post to take one touch, before slamming the ball into the back of the net on the half-volley.
Rovers continued to call the shots and visiting keeper Mark Bunn had to save at full stretch from Paul Green four minutes later, after Jason Price and McCammon had set up the chance.
Town's big striker Poul Hubertz was well contained throughout by centre-backs Steve Roberts and Adam Lockwood and the threats from the visitors were few and far between.
They only managed one shot on target in the first half and Andy Kirk's 20-yarder was saved by Neil Sullivan at the foot of the post.
There was little respite for the Cobblers and Rovers made it 2-0 in the 29th minute when Lockwood headed home in fine style at the near post from Brian Stock's cleverly flighted corner kick.
Town looked more determined in the second half, but there was no end product to their hard work and on-loan striker Dean Bowditch headed into the sidenetting from Joe Burnell's left-wing cross.
Rovers were desperately unlucky not to add a third in the 49th minute when Steve Roberts twice headed against the crossbar in quick succession in a goalmouth scramble following a corner.
Town never looked like fighting back although Jason Crowe missed a good chance when he fired straight at keeper Sullivan from close range seven minutes from time.