Rovers boss Ray Graydon left the pitch to chants calling for his dismissal after Northampton had completed a battling comeback.
Home fans shouted 'We want Graydon out' as their disappointing season continued, while the 532 Cobblers fans celebrated a late Christmas present.
It looked as though Rovers were going to profit from a gift when they were rewarded a dubious 47th minute penalty as Lewis Haldane went down under challenge from Chris Hargreaves.
Wayne Carlisle produced a perfectly struck spot kick which gave goalkeeper Lee Harper no chance and it was the perfect start to the second half for Graydon's men.
But they were made to pay for two glaring misses by striker Junior Agogo as Northampton found some spirit in the blustery and wet conditions.
Substitute Derek Asamoah volleyed a 70th minute equaliser after good control and a clever through pass from Martin Smith.
And four minutes from time Rovers were exposed at the back by Chris Willmott's header forward which allowed Richard Walker to break clear and shoot low past Kevin Miller.
By then Agogo had been substituted after an afternoon to forget. He hit a post when it looked easier to score on 11 minutes and was guilty of another bad miss on 62 minutes.
This time he shot too close to goalkeepeer Harper to the frustration of the mass ranks of Rovers fans behind the goal.
Both sides had narrow escapes in the first half, with Des Lyttle clearing off the line for Northampton and Christian Edwards doing the same job for Rovers.
Both sides found control difficult as the rain became heavy and swirled around the Memorial Stadium.
Rovers looked in control for an hour, but the final 30 minutes belonged to Northampton and they always looked the more likely scorers in the closing stages.