The young Reds had led twice through Elliot Simoes and Mateo Aramburu either side of the break, but were pegged back by Harry Forster’s penalty and Joy Mukena’s header two minutes from time.
It’s a result that means Martin Devaney’s side finish the season seventh and 12 games unbeaten following a remarkable run of form in the New Year.
The visitors started much brighter and Victor Adeboyejo took aim on a couple of occasions from range, but was unable to test Adam Parkes in the Watford goal.
Elliot Simoes then had a sighter from the edge of the area, but his effort fizzed narrowly wide of the upright as Barnsley continued to search for the opening goal.
It eventually came midway through the half as Matty Wolfe burst down the left flank and pulled the ball back for Simoes, who casually curled home into the far corner.
The Hornets were stung into action and came close to equalising through Connor Tomlinson, but his point-blank header was brilliantly tipped palmed away by Niall Clayton.
Forster was next to be denied by the Reds’ stopper as his low drive was tipped onto the post as the first half drew to a close.
Chances were few and far between for large parts of the second half, but the game soon burst to life once more when the hosts were awarded a penalty 13 minutes from time.
Forster confidently stepped up to convert, sending Clayton the wrong way to set up a thrilling finale at Vicarage Road.
Two substitutes then combined as Barnsley restored their lead, with Amir Berkovits threading an inch perfect pass for Aramburu to surge onto before finishing with aplomb into the bottom corner.
But the Reds were unable to hold onto that advantage as, just minutes later, Mukena was left unmarked to nod home from close range and claim a share of the spoils.
WATFORD XI: Parkes, Balogun, Green, Ochieng, Mukena, Weaire, Blair, Yamfam, Tomlinson, Wise, Forster.
Subs: Hoskins, Leighton, Spyridis, Taylor, Crichlow.
REDS XI: Clayton, Gagen, Fielding (c), Heaven, Calligan, Mendes Gomes (Berkovits, 58), Wolfe, Bird, Simoes, Adeboyejo (Aramburu, 70), Vickery-Taverner (Sang, 46).