Things looked desperate for Steven Schumacher’s side as they lost a 1-0 lead and had Jordi Osei-Tutu sent off within a few minutes of the restart.
David Kasumu had equalised Eoin Toal’s 14th minute header before Marcus Harness scored from the spot.
Kasumu then added a third for the Terriers, who with a man advantage looked odds-on to claim a win which could have reignited their play-offs chances.
But after Johnny Kenny smashed in Bolton’s second with 13 minutes of normal time, the 10 men were rejuvenated by the sight of eight minutes of stoppage time. And with the timewasting shenanigans continuing beyond that point, it was left to substitute Cissoko to score a brilliant curling effort timed at 101 minutes.
Wanderers named an unchanged side from the one that beat Stevenage 5-1 in midweek. John McAtee returned on the bench in place of Kyle Dempsey.
Schumacher will have had few complaints with the first half performance and the Whites fully deserved to be ahead at the interval, thanks to Eoin Toal’s thumping header 14 minutes in.
In truth, they should have been much further ahead, particularly as two golden chances had fallen to their top scorer, Sam Dalby.
The first came from Johnny Kenny’s persistence to win the ball in the Terriers half, he released Gale, whose pin-point cross was stabbed wide.
Dalby then had his head in his hands once again after Ruben Rodrigues’s cross was flicked by Kenny into his path at the far post, only for the shot to end up in the South Stand.
Huddersfield had occasionally threatened, Lasse Sorensen flashing one header right across Bolton’s six yard box but with the hosts playing some incisive stuff at times it hard to see anything coming other than the win that would have all-but sealed a play-off spot.
Dalby had yet another chance after the restart, fed by Johnston, his angled shot was blocked well by the advancing Alnwick.
And Bolton were made to pay very dearly for their wastefulness. Kasumu bundled in his first goal of the season after Radinho Balker had knocked down Cameron Humphreys’ cross.
A minute later Sorensen rolled in another dangerous cross and when Osei-Tutu tugged on Kasumu’s arm, he was handed a straight red card. Harness send Bonham the wrong way from the spot to make it 2-1.
The game seemed well beyond Wanderers’ grasp as unlikely goal source Kasumu grabbed another, his shot bouncing off Johnston’s ankle and leaving Bonham helpless.
Wanderers were not prepared to go down without a fight, however, and particularly Kenny, who smashed in his fourth in four games from a tight angle to set up a grandstand finish.
Erratic referee Jacob Miles made sure nobody knew where they stood in stoppage time, angering both sets of fans with his decision making.
And just as it looked as though Bolton’s last chance had gone with Max Conway putting a cross high into the stands, Cissoko was fed by Cozier-Duberry to curl his fifth goal of the season and spark scenes of pure joy around the stadium.
The draw equals the club record 17 draws in a season set in 1991/92.
