Goal by Magno Vieira and Martin Smith earned the Cobblers a second league double over West Country opposition in the space of five days.
Brazilian-born striker Vieira, in the last week of his first month's loan spell from Wigan, opened his scoring account on the half hour after a mix-up in the Bristol Rovers defence.
Chris Carruthers had lobbed the ball forward, Marc Richards applied the flick-on before a tangle between goalkeeper Kevin Miller and defender Adam Barrett allowed Viera to stroll the ball into an unguarded net.
The killer second arrived 13 minutes from time when Smith struck a free-kick from the edge of the penalty area which took a deflection off the Rovers wall to give the former Huddersfield man his 11th goal of the season.
This was Rovers first defeat in three matches under the caretaker charge of Phil Bater and although they missed a few clear cut openings, they failed to test Lee Harper in the home goal.
Northampton were briefly in trouble in the 11th minute when Paul Trollope lost possession, allowing on-loan striker Lee Matthews a clear run on goal, but he put his shot horribly wide.
Rovers' only other chance of note arrived 12 minutes from time when former Northampton man Dave Savage cut through the home defence, but again failed to hit the target from a decent position.
Rovers had penalty appeals turned down when sub Junior Agogo tumbled in the box after apparently making contact with Harper, but the referee waved play on.
Northampton were good value for their victory and could have added to their tally, especially if Richards had enjoyed more luck in front of goal.
The hapless Richards saw a ricochet off Miller's knees strike him a minute after the break, the ball flying wide of the target.
And the striker hit the crossbar after showing a neat touch eight minutes from time as he brought down a decent cross from Trollope.