Eoin Doyle and Antoni Sarcevic scored first-half goals as Ian Evatt’s Whites produced their best display of the season to make it 10 games unbeaten and 26 points from a possible 30.
Matt Gilks’ mistake allowed Kyle Knoyle to pull a goal back but Bonner conceded the hosts had been excellent on the night and “above a level” his second-in-the-table side had faced.
“You don’t come here and dominate possession because Bolton are really good at it,” he said.
“We started well and had a couple of good counter-attacking moments but we found it hard.
“You have to respect the way they play, the way they run and move the ball and the speed they play at. It was above a level we have played against this season.
“We have to be intelligent enough to understand why we lost and humble enough to know they are a good side. We have to learn from them and the things they did well.
“There is a proper squad here and this is a really big club which shouldn’t be at this level. If they keep playing like that they won’t be at this level too long.”