Having lost 2-0 in the league but won by the same score in the FA Cup in London, Rovers went behind as Marquis's diving header deflected Igor Vetokele's cross-shot into his own net in the 72nd minute but Wilks soon fired them level.
Marquis was then denied a stoppage-time winner by a hotly disputed offside decision.
Rovers chief Grant McCann made changes as he attempted to cut the gap on the fifth placed-Addicks, who began five points clear but having played a game more than the hosts.
Midfield play-maker Herbie Kane resumed after a groin injury but central defender Tom Anderson missed the game due to serving a concussion protocol.
McCann, who had made three changes for the midweek 2-0 defeat at Shrewsbury - Aaron Lewis, Tommy Rowe and Tyler Smith replacing Kane, Matty Blair and James Coppinger - brought in central defender Andy Butler and restored Kane and Coppinger to the starting line-up.
Charlton manager Lee Bowyer began a three-match touchline ban for abuse of the referee in the 46th minute of the 2-1 win at AFC Wimbledon - their first win in five games. He brought back defensive midfield man Krystian Bielik after a two-match suspension for picking up 10 bookings.
The game kicked off with second-placed Barnsley having gone further clear of the pair, courtesy of their tremendous 3-0 early kick-off win at Southend despite having had Jacob Brown sent off in the 35th minute.
Only a series of fine defensive blocks prevented Charlton from taking an early lead their fast-flowing attacking play merited.
Lyle Taylor almost drove them ahead in the 20th minute after Jonny Williams had nodded the ball into the area but Marko Marosi blocked with his legs.
In reply, John Marquis broke down the left and crossed but the ball bounced wide off Mallik Wilks as Rovers had to rely on a counter-attacking threat.
From one such ploy, Coppinger split the defence to send Marquis racing into the area but Patrick Bauer slid in to deflect the shot over the bar.
Marquis also clipped the ball over from 12 yards after being fed in by Danny Andrew but the flag was raised in any case.
The striker was narrowly offside again as he converted a cross from Wilks in the 32nd minute as Doncaster finally got on top.
Bielik, however, almost volleyed Charlton ahead after having had his initial effort blocked but Marosi did well to tip his effort over for a corner.
The half ended goalless and neither side made a change at the break.
Joe Aribo curled a shot over the bar in the early stages of the second half and Coppinger had a shot deflected for the first of two successive corners for Rovers - the second of which saw Paul Downing's far post header cleared off the line by Chris Solly.
Matty Blair replaced Crawford in the 59th minute and took his midfield slot.
Tarique Fosu replaced Williams much to Doncaster's relief in the 62nd minute.
Charlton cranked up the pressure and Taylor struck the base of a post before Aribo's shot was deflected for a corner from which Cullen played it short to Igor Vetokele, whose cross-shot was met by a diving header into his own net by Marquis in the 72nd minute.
Five minutes later and Rovers were level as the ball fell for Wilks found space on the edge of the area and he drilled the ball inside Dillon Phillips's left-hand post.
Rovers immediately made a double susbtitution, Rowe and Alfie May replacing Kane and Coppinger.
May was denied a penalty when his shot struck the hand of Bielik and then Phillips made two fine saves down to his left from Marquis and Lewis as Rovers pressed for the winner.
It looked as though Rovers had won it in the sixth minute of stoppage time when Ben Whiteman rattled the bar and the ball fell for Marquis to curl the ball home only to be denied by the linesman's flag, much to the home fans' fury.
The draw meant that Peterborough had increased the pressure on both sides with victory over Wycombe.