Paul Trollope's side appeared to have been undone by Dennis Lawrence's 70th-minute finish for in-form Crewe.
But it was the Railwaymen who were left hanging on at the end as Craig Disley headed a corner onto the bar before home keeper John Ruddy produced an excellent save to deny substitute Jo Kuffour.
The game took time to warm up but when it did it was an end-to-end affair.
Crewe were handicapped by the loss of striker Calvin Zola with an injury in the 27th minute.
But they roared back and appeared to have taken the lead two minutes before the interval when Marlon Broomes' overhead kick was only pushed out by Rovers keeper Steve Phillips. Joel Grant finished the rebound high into the net but the goal was chalked off for offside.
Rovers posted a warning on the stroke of half-time when League One's leading scorer, Rickie Lambert, headed inches over from a Clayton Donaldson cross.
Broomes went close with a header from a Billy Jones free-kick just before the hour mark as Crewe improved on their first-half showing.
Icelandic Under-21 international Gylfi Sigurdsson was instrumental in much of the home side's forward play but Rovers winger Jeff Hughes was equally dangerous on the break.
Referee Andy Warmer enraged the home support with some inconsistent decisions. He missed several handballs and was badly positioned in the six-yard box when a Crewe effort struck cannoned off him amid a furious melee. By then both sides had scored.
Jones's long free-kick was headed on and Donaldson crashed a shot on to the bar before Lawrence rolled in the rebound for the 70th-minute opener.
But Rovers were level within four minutes when substitute Jo Kuffour clipped the ball on to the far post where Duffy was running in to ram the loose ball high into the net.