Rovers boss Tony Mowbray was left ruing missed chances as his side missed the chance to make it seven consecutive wins.
Mowbray's men weren't at their fluid best against the Cobblers, with Bradley Dack equalising after Aaron Pierre's opener.
However, Rovers couldn't take their late opportunities, with Craig Conway and Marcus Antonsson both missing opportunities to win the game for the visitors.
"I'm disappointed to only take a point. We just couldn't get to our usual intensity or levels," Mowbray said honestly after the game.
"I don't want to make excuses or a deal of things but I do believe illness in the camp was a reason for our lack of energy.
"Craig's apologised for missing the chance just before Marcus saw his penalty saved.
"Marcus felt confident and unfortunately missed his kick. We haven't played as poorly as that for a very long time."
But despite being frustrated, Tony admitted the hosts were deserving of their point for their hard work and determination.
"You have to give credit to Northampton. They were a physical threat and worked extremely hard for their manager.
"We're left frustrated to only take the point home with us. We have to get on with it. We did enough to take the points but didn't take our chances.
"It was an opportunity for us to keep things rolling on but it wasn't to be. There are still plenty of games to come for us."