Tommy Rowe missed the decisive spot kick as Rovers suffered penalty shootout disappointment in the first knockout stage of the Checkatrade Trophy for the second consecutive season.
With Rochdale ahead 5-4 in the shootout, Rowe saw his penalty comfortably saved by Rochdale keeper Josh Lillis to send the Lancashire side through to the third round.
Rovers showed good character to fight back from behind in the second half with Liam Mandeville equalising smarlty after Matthew Gillam scored a penalty for the hosts.
But they will ultimately rue their failure to take early chances after a red hot start on an ice cold night at Spotland.
Darren Ferguson continued to show his admiration for the much-maligned competition, even naming a stronger than expected side.
While he made eight changes, his starting XI was made up entirely of senior players, operating in the 3-4-3 system that served the club well until the 3-0 defeat at Wigan Athletic the week prior.
Rochdale boss Keith Hill was similarly intent on advancing to the third round and made only four changes from his side’s win over Peterborough United.
Packed with youthful energy, Rovers made a strong start to the game and almost took the lead mere seconds in.
Sweeping forward from the kick off, Harry Toffolo’s deep cross found Matty Blair who smashed first time from the corner of the box, only for Kgosi Ntlhe to block on the line.
Rochdale scrambled back to clear again moments later when Joseph Bunney blocked Alfie Beestin’s driven shot at the back post.
Rovers were surging forward quickly and with numbers as they looked to catch the hosts cold.
Matty Blair slid a pass through for Mandeville who fired low only for Rochdale keeper Josh Lillis to save comfortably.
Rochdale fired their first warning shot after 12 minutes when Callum Camps curled inches wide from the edge of the area.
But Rovers continued to have the better of proceedings and Niall Mason saw a header blocked by his own man, Mathieu Baudry.
Ben Whiteman got into a superb position to meet Blair’s through ball but struggled to get his shot away and struck tamely at Lillis.
Rovers’ failure to make opportunities count was punished just after the half hour mark when they conceded a penalty as Harry Toffolo felled Andrew Cannon.
Gillam slotted calmly into the bottom corner, sending Marko Marosi the wrong way.
While harsh on Rovers, they failed to respond and struggled to find the same zip to their play after falling behind.
It allowed Rochdale to establish control of the game for the first time and they began to look after the ball well.
Dale should have doubled their advantage in first half stoppage time when Cannon surged into the box from the right but sliced his shot out for a throw in from 15 yards.
Rochdale started the second half the stronger and it took a fine save from Marosi to keep out a dipping drive from the impressive Camps.
The hosts pressed incredibly well, penning Rovers into their own half and denying them any real time on the ball.
It was proving to be a lacklustre half from a Rovers perspective, which forced Ferguson’s hand. He sent on Andy Butler - against his original intentions - for the final 25 minutes, switching system to a 4-4-2.
And it quickly made the difference.
Tyler Garratt was sent charging forward on the left only to be closed down as he reached the box. That proved to be a warning shot as Rovers levelled on 73 minutes.
A fine through ball sent Mandeville into the box and he fired confidently under Lillis to level the score.
The game opened up after the equaliser but both sides struggled to force the opposing keeper into a save.
But Baudry was required to head off the line in stoppage time to keep out Jordan Williams’ looping header.
It sent the game to the shootout. Niall Mason, Mandeville, Issam Ben Khemis and Craig Alcock all scored from the spot but the pressure was on Rowe as Rochdale netted all five.
With his first touch of the game after replacing Ben Whiteman in stoppage time, he send a tame effort which Lillis caught easily.
Rochdale: Lillis; Cannon, McGahey, McNulty, Ntlhe (Kitching 41); Ashead; Camps, Bunney; Rathbone (Inman 80); Andrew, Gillam (Williams 56). Subs not used: Moore, Rafferty, Slew, Morley.
Rovers: Marosi; Alcock, Baudry, Garratt; Blair, Mason, Whiteman (Rowe 90), Toffolo (Butler 68); Beestin, Mandeville, Ben Khemis. Subs not used: Lawlor, Prior, James, Scattergood, Morris.
Referee: Darren Handley (Lancashire)
Attendance: 786 (103 away)