Barnsley had the better of the opening half but the Merseysiders were strong in the second period after sending on Eugene Dadi and David Beresford in a change of tactics. It seemed Rovers would secure their ninth home victory when Ian Hulme put them ahead in the 73rd minute with a well-struck shot from 12 yards from a Dadi knock down after good work by Ryan Taylor.
But then in injury time Barnsley put in a last-ditch effort and a left-wing cross by Tom Williams was met by Antony Kay who found the target from just inside the box.
The game ended on a sour note with a number of players squaring up to each other and the Tranmere trio of Hulme, Paul Hall and Mark Rankine were all cautioned.
Kay had also gone in the book for over celebrating after his goal. Michael Chopra saw and early shot for Barnsley blocked out and then Michael Boulding's shot was held at the second attempt my keeper Russell Howarth.
Boulding heading into the side heading then Shuker was denied by an excellant block by Taylor.
Tranmere might have been ahead on the half hour but a downward header by the unmarked Mike Jackson, from a corner saw the ball bounce agonisingly over the bar.
Tranmere began to get a grip on proceedings after the break but Beresford fired over and then Dadi found the top netting with a header from a Jason McAteer centre.
Boulding was inches wide from 20 yards for Barnsley before Tranmere's Hall failed to find the target from just six yards. But the action stayed exciting to the end in front of Tranmere's biggest gate of the season. Taylor was super for Rovers. Skipper Tony Vaughan set a big example for Barnsley.