Rovers’ No 9 sent the keeper the wrong way from 12 yards for his third goal of the season after Lee Tomlin was brought down in the box by Shaun McWilliams.
And Miller should have doubled Doncaster’s advantage late on when he ran through one-on-one, only for a last-ditch tackle to thwart him.
Danny Hylton might have then equalised for the Cobblers but headed wide from six yards out.
The result lifts Gary McSheffrey's side into the automatic promotion places after six games, of which they have won four.
Here’s how we rated the Rovers players.
1. Doncaster Rovers player ratings
Doncaster's Bobby Faulkner challenges for the ball against Northampton Town. Photo: Howard Roe/AHPIX LTD
2. Jonathan Mitchell - 7
Some poor distribution at times in the first half but claimed anything that came into his 18-yard box very well and saved from Northampton's previously red-hot striker Sam Hoskins late on. Photo: Howard Roe/AHPIX LTD
3. Tommy Rowe - 7
Solid at left-back and limited Northampton to very little. Not quite as effective going forward in the first half but became more of a threat after the break. Photo: HOWARD ROE, Howard Roe/AHPIX LTD
4. Kyle Knoyle - 7
Kept the country's top-scorer very quiet all afternoon. Excellent defensively and supported the attacking effort well. Best performance of the season so far. Photo: Other 3rd Party