David Ngog had a great chance to give the home side the lead inside the opening five minutes but he could poke Darren Pratley's cross wide from six yards out.
Rovers threatened after half time and again it was through Hanley, this time his header clattered off the bar.
Bolton responded through Prately who made a surging run through the middle of the Rovers defence but could only put his shot wide.
The Trotters nearly paid for those misses when Pedersen struck a vicious shot which looked to be creeping in but Andy Lonergan got a hand to it and tipped it over.
Bolton finally broke the deadlock in stoppage time as substitute Eagles's low shot trickled into the bottom corner with the aid of the post, which was enough to win them the game.