Wanderers, who themselves have been on a poor run of form which had not seen them win since the opening day, took the lead in the fourth minute through midfielder Nigel Reo-Coker, who converted Chris Eagles's cross.
Roberto Martinez responded positively to falling behind and levelled up proceedings five minutes before the break through Mohamed Diame. The centre-midfielder's shot from distance nestled in the net after deceiving Wanderers keeper Jussi Jaaskelainen.
However, Diame's strike was not enough for the home side to head into half-time all square. Bolton front pair Kevin Davies and David Ngog linked for the latter to score from close range two minutes into stoppage time.
Owen Coyle's visitors spurned a number of chances to extend their lead further after the restart.
The third goal eventually arrived in deep into time added on, with winger Eagles claiming his first Premier League goal for the club.