Pratley went closer with his next attempt – his acrobatic effort was just off target after Joe Mason's strike had deflected into the path of his teammate on 17 minutes.
Neil Danns spurned a good opening for Bolton after the break when he fired straight at the goalkeeper after a good cross from Beckford.
However, the former Crystal Palace winger made no mistake minutes later when he converted to give the Trotters the lead.
Substitute Mark Davies made it two 15 minutes later by calmly finishing past Button after a mazy run.
Jon-Miquel Toral gave the visitors hope with a goal seven minutes from time, but Craig Davies restored Bolton's two-goal advantage in stoppage time as they earned a first home win under Lennon's management.