Wanderers looked to be heading for victory after on-loan forward Lukas Jutkiewicz opened the scoring in the first half, and the Latics never really got going until Manchester United loanee Nick Powell scored just before stoppage time.
Callum McManaman then won a penalty in time added on, but Jordi Gomez's spot-kick was heroically saved by Trotters keeper Bogdan.
Bolton named new loan signing Andy Robinson on the bench while Alan Hutton made his final loan appearance from Aston Villa at right-back.
Shaun Maloney and Gary Caldwell were not risked by Wigan, despite being on the verge of a return after lengthy spells on the sidelines.
The home outfit got off to a flying start, with Robert Hall testing former Trotters stopper Ali Al-Habsi within the first minute of the game - Al-Habsi nervously fumbling the effort before grasping the ball.
Al-Habsi was called into action again as Liam Trotter brought the ball down to Jutkiewicz on the half volley. This time the Egyptian international proved his class with a magnificent diving save.
It was not all one-way traffic, though, and the Latics could have scored through both Emmerson Boyce and Marc-Antoine Fortune had it not have been for heroic blocks from David Wheater and Jay Spearing.
A magnificent assist from Hall then saw Bolton take the lead. The former West Ham winger's free-kick was curled perfectly into the danger area and just needed the slightest touch from Jutkiewicz to beat Al-Habsi.
They then almost doubled their advantage before half-time, with Trotter and Jutkiewicz combining again. This time the English striker failed to guide the ball on target from a tight angle.
The second half started in similar fashion to the first with Hall once again challenging Al-Habsi, who tipped his powerful strike over the bar.
Wigan were then fortunate to keep 11 players on the pitch. Lee Chung-Yong broke clear before last-man Leon Barnett brought the South Korean down on the edge of the penalty area. Referee Darren Drysdale, though, only chose to award the defender a booking.
However, that did not stem a change in the tide as Wanderers continued to look the more likely side to score next.
It took a string of top saves to stop them doing so. Hall, Wheater, Tim Ream and Jutkiewicz were all denied by the acrobatics of Al-Habsi, who was in inspired form on his return to the Reebok.
Despite coming on stronger in the later stages, the visitors never really tested Bogdan in the Trotters goal until Powell smashed in an equaliser before injury time, with Martyn Waghorn cutting the ball back to the former Crewe midfielder in the box.
Alex Baptiste then gave away the late penalty but Bogdan saved to stop Bolton from unfairly losing the match.