The Cobblers have now scored just five goals in ten League One matches and manager John Gorman is at his wits end in trying to solve the dilemma.
But Rovers are on an upward spiral and they made it two wins on the road inside five days following their 4-0 demolition of Brentford on Tuesday night.
They left it late, with last season's top scorer Heffernan applying the finishing touch with his head to a cross from Brian Stock following a short corner move before Guy made the most of a mistake by Luke Chambers to sprint clear of the home defence and coolly beat Mark Bunn for the second.
Bunn's opposite number Neil Sullivan is on loan from Leeds and he had to make two critical stops from Andy Kirk when the scores were goalless.
They came either side of half-time with Kirk sweeping a first-time shot from a Nick Wright cross three minutes before the break only for Sullivan to show excellent reflexes to tip the ball over the crossbar.
Sullivan knew far less about the second save four minutes after half-time when Kirk burst through on goal but although he went the wrong way, he saved the ball with his knee.
Northampton's other chances came at either end of the game, with Pedj Bojic seeing a dipping shot just clear the crossbar in the tenth minute while a late header from substitute Ryan Gilligan lacked the venom to seriously test Sullivan.
Doncaster's best other moves saw Mark McCammon denied by a brilliant saving tackle by Andy Holt while Paul Green volleyed disappointingly wide in the 17th minute.
Twelve minutes after the restart Doncaster should have gone ahead when a pass from James O'Connor put Jonathan Forte in the clear but the midfielder failed to hit the target with his angled drive.
Then Stock almost gave the travelling support something to cheer with a fierce 30 yarder which brought a fantastic save by Bunn.