Rovers booked their place in the third round of the EFL Cup in a topsy-turvy encounter at Ewood Park.
It took extra-time and the odd goal in seven before Rovers ensured it would be their name in the hat in Wednesday night's draw.
A stunning opener from Billy Bingham put the visitors in front, with Rovers regretting missed chances as Crewe added a second when Chris Dagnall snapped up a rebound following David Raya's fumble.
But a Hope Akpan goal towards the end of the first half gave the home side some impetus, Scott Wharton adding to his burgeoning reputation by firing Rovers level on 69 minutes.
Craig Conway then spectacularly put Rovers in front for the first time on the night, but Crewe came back, taking the tie to extra-time as Dagnall netted once more.
But following a series of corners where Rovers came close, it was Shane Duffy who popped up with the vital goal to send Rovers through.
As promised, Owen Coyle rang the changes from the side that faced Burton Albion at the weekend with David Raya, Liam Feeney, Anthony Stokes and Shane Duffy all coming into the side. Jason Steele, Gordon Greer, Ben Marshall and Danny Graham the men to make way.
Whilst the visitors made just the two changes from their draw with Newport County on Saturday as Callum Saunders and Danny Hollands replaced Ryan Lowe and James Jones.
Under the Ewood lights for the first time this season it was Rovers who were lively from the off. Just two minutes in and Feeney and Sam Gallagher combined well down the right, but the ball across the box was cleared in the nick of time by Oliver Turton with Stokes poised to find the back of the net.
Then Feeney raced away down the left before cutting inside on his right foot, but his attempted curler flew just beyond the far post.
But despite the bright start from the home side, it was the Railwaymen who were celebrating taking the lead after just eight minutes with a goal of the highest quality.
As Rovers backed off in the centre, George Cooper teed up Bingham and the midfielder hit the sweetest of shots as it flew into the top corner from fully 30-yards.
It took a while for Rovers to regain their composure as the Alex grew in confidence, but the visitors did have keeper Ben Garrett to thank with a fine stop from a powerful header by Duffy.
Gallagher then fired wide after latching onto a through ball by Conway, but just as it looked like the home side would start to impose themselves once more they conceded a soft second on 39 minutes.
Goalscorer Bingham let fly from distance, but Raya fumbled the bouncing ball and that allowed Dagnall to pounce from close range.
But Crewe's two-goal advantage would only last 90 seconds as Rovers reduced arrears. Jason Lowe with a perfectly weighted through ball for Hope Akpan and he slipped it under Garratt to give the blue and whites hope going into the break.
Unchanged at the turnaround, Rovers should have been level on 48 minutes as Conway played Stokes in on on goal, but whilst the Irishman was crowded out, he fed Gallagher, however the on-loan striker saw his shot blocked.
But despite that early second half scare, the visitors could have made it 3-1 on 51 minutes as Cooper saw a shot from 12-yards crash off the woodwork, before Callum Saunders saw his close-range effort spectacularly saved by Raya.
That prompted a double change for Rovers as Danny Graham and Danny Guthrie replaced Anthony Stokes and Jack Byrne, Guthrie soon in the thick of the action with a shot that curled wide.
After knocking on the door repeatedly, Rovers were finally back on level terms on 69 minutes. Conway with a corner from the left, Scott Wharton rising, and although the youngster saw his initial header strike the bar, the defender, who only made his debut on Saturday, had the awareness to force home the rebound.
Boosted by the equaliser Rovers went in search of the next goal, Graham inches wide of the target with a stinging shot from the edge of the area, before a miscued punch from Garratt needed to be hacked off his own line by Zoumana Bakayogo.
But the visitors still carried a threat as Raya had to dive to keep out low drive from Alex Kiwomya.
Two minutes from time Rovers thought they had grabbed the all-important goal to book their place in the third round. Liam Feeney sent a ball to the far post to where Graham headed back across goal and Conway showed great acrobatics to hook the ball into the net.
However there was still time for a sting in the tail as deep in added time at the end of the 90 the Railwayman struck once more.
Stephen Hendrie mis-placed a clearing header straight to Kiwomya and he found Chris Dagnall who in turn found the bottom corner to ensure extra time.
But as dramatic as the proceeding 90 minutes had been, the 30 minutes of added time saw Rovers dominate.
A series of corners from Conway would lead to the home side regaining a lead that they thankfully wouldn't relinquish a second time.
Successive deliveries from the Scot saw a Gallagher header tipped over, a goal bound shot from Wharton cleared off the line, and a near post header from Graham deflect wide. But corner number four would see the ball finally nestle in the back of the net when Duffy saw his header squeeze home.
Duffy went close to extending the Blues' advantage with a powerful header from a Hendrie cross in the second half of added time, whilst Feeney fired over after a Conway inspired break.
To their credit Crewe pressed until the end, but Rovers held out to book their place in Wednesday night's third round draw.
ROVERS: Raya, Lowe (c) (sub Marshall 70 mins), Duffy, Wharton, Hendrie, Feeney, Byrne (sub Guthrie 56 mins), Akpan, Conway, Stokes (sub Graham 56 mins), Gallagher.
Subs not used: Steele (GK), Greer, Mahoney, Doyle.
Goals: Akpan 41 mins, Wharton 69 mins, Conway 88 mins, Duffy 97 mins.
Booked: Guthrie 90+1 mins, Gallagher 103 mins.
CREWE: Garratt, Turton, Guthrie, Davis, Dagnall (c), Saunders (sub Lowe 65 mins), Cooper (sub Ray 79 mins), Bakayogo, Hollands (sub Jones 77 mins), Bingham, Kiwomya.
Subs not used: Richards (GK), Nugent, Kirk, Ainley.
Goals: Bingham 8 mins, Dagnall 39, 90+3 mins.
Attendance: 3,448 (including 535 visiting supporters)