The home side had dominated for the vast majority of the contest, only to fall behind 20 minutes from time when Tom Walker’s shot was deflected past a helpless Ali Al Habsi for the opener.
It was a crushing blow for a Wigan side that had hit the bar in the first half through James Perch, had a Leon Clarke goal chalked off for offside and seen Marc-Antoine Fortune fluff a relatively straight-forward heading chance.
But they stuck to their task in the second period, and after Ben Amos had denied Jermaine Pennant with a stunning stop, the goalkeeper then tipped a Clarke header on to the bar as well as clawing away a Sheyi Ojo effort.
It looked like time would run out on Wigan, but in the fourth of five added minutes, Waghorn equalised with a goal that could yet save their season.
Wigan had started the game on the front foot, with Bolton content to play on the break. And the visitors showed their threat inside the early exchanges when Adam Le Fondre led a breakaway only for Gaetan Bong to save the day in the nick of time.
Wigan were getting the ball wide at every opportunity to wingers Josh Murphy – making his full debut – and Pennant. But it was through the middle that they nearly broke the deadlock, with Perch’s 30-yard effort beating Amos only to hit the bar and come back out.
The ball fell invitingly for Clarke, but the striker’s header was weak and straight at Amos.
At the other end, Walker could not make the most of Liam Feeney’s cross, and the same player was unable to make amends moments later when he fired past the post.
Former Wigan man Emile Heskey had a great opportunity to open the scoring on the half-hour mark but his free header from a corner flashed past the upright.
Latics ended the half on a high and should have taken the lead when Murphy’s pinpoint cross found Fortune, whose header from point-blank was straight at Amos when either side would surely have brought about the opening goal.
Wigan did have the ball in the net right on half-time through Clarke, but the striker looked well offside and the flag was up on the far side.
The home side picked up where they left off after the restart, and a Pennant free-kick bound for the top corner was superbly clawed out by Amos.
Pennant then had time and space in the box to pick his spot on the edge of the area, but his shot hit Clarke and was hacked away to safety.
The visitors won a couple of corners but they were virtually non-existent as an attacking force, with Wigan asking all the questions.
But with 20 minutes to go, the unthinkable happened and Wanders took an undeserved lead in extremely fortuitous circumstances.
Walker’s shot from distance took a massive deflection off a defender, completely wrong-footing Al Habsi and rolling into the net to the delight of the packed away end behind the goal.
Credit goes to Wigan for the way they stuck to their task, and Amos produced another fabulous stop to deny substitute Ojo before Clarke saw a header tipped on to the bar by the goalkeeper.
It looked as though Bolton were going to hold on for all three points before, in the fourth added minute, Waghorn sent an overhead kick in off the bar to rescue a point for the hosts.
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