A goalless first half was followed by a Steven Davies goal shortly after the break, when he followed up on his own blocked cross to fire Dale into the lead.
Jamie Allen struck the post with a header shortly afterwards, whilst Josh Vela’s deflected shot struck the woodwork for the visitors in the dying minutes.
Four minutes were added on, but Dale held on for a memorable three points after a fantastic team performance.
Harrison McGahey and Donal McDermott made way for Joe Rafferty and Jamie Allen, in two changes from Saturday’s win at Millwall.
The first half was hotly contested and evenly matched, with a healthy attendance inside the Crown Oil Arena making for a feisty atmosphere.
Whilst clear opportunities were few and far between, the opening stages ensured an entertaining first period.
Joe Thompson’s deep cross almost crept in at the far post as it evaded everyone, whilst Chris Taylor’s shot for the visitors deflected into the arms of Josh Lillis.
The best chance of the half fell to Bolton, through James Henry. A break down left saw Jamie Proctor cross to the far post, but as Henry slid in he miscued his effort wide of Lillis’ right post.
Ian Henderson was forced off in the 27th minute, due to a head injury sustained in a first minute challenge. Steven Davies replaced him up front.
Dale ended the half strongly, with a Jamie Allen shot from a corner kick well over, before Jay Spearing forced Lillis into a good save with a crisp shot from distance in added time.
The second half started with a bang, as Dale took the lead just seven minutes in. Davies’ cross from the right was blocked back into his path, and running on to the ball he lashed a first time effort into the roof of the net.
The lead was inches away from being doubled five minutes later, when Allen struck the post with a header. Matthew Lund crossed from the left and Allen’s glancing header struck the inside of the post, before Davies’ rebound was blocked away.
David Wheater turned a free-kick wide at the near post for Bolton, before an almighty scramble in their own area was eventually cleared after Mark Howard had dropped a cross.
Lillis was forced into a save for the first time in the second period with little over ten minutes left. A cross from the left found its way through to Henry at the back post which he turned goalwards, but
Lillis scrambled across the line on his knees to palm the effort wide of goal.
Sanmi Odelusi replaced Thompson for the final ten minutes with Dale’s second change, but with four minutes remaining the visitors struck the post with a deflected effort.
Substitute Josh Vela’s shot at the far post was deflected by Bunney, and the ball looped over Lillis and off the inside of the post before being cleared.
Four minutes of added time were played, which Dale defended resolutely as Bolton loaded the box, to hold on to a memorable victory.