The 35-year-old turned his marker and headed home a cross from Marc Bridge-Wilkinson just moments after Deon Burton had fired the Millers into a deserved 80th minute lead.
Rotherham dominated the match with their smooth passing football and should have had the victory sewn up long before then.
Jamal Campbell-Ryce and Paul McLaren both had shots blocked on the line in a one sided first half in which City goalkeeper Donovan Ricketts limped off injured.
His replacement, Russell Howarth, then pulled off a stunning save from a free-kick by Michael Keane to keep the scores level and City were endeared to a fine performance by skipper David Wetherall, who lead by example at centre half.
Bradford looked livelier after the interval and Windass was twice denied by home keeper Neil Cutler, first from a fierce 20-yarder and then from a close range header.
Burton, a close-season signing for Rotherham from Brentford, thought he had won it for the home side when he hammered in his first goal for the Millers after being set free by a long, raking pass from centre-half Shaun Barker.
Windass popped up to nod the equaliser just three minutes later and a rejuvenated Bradford side swept forward in search of a winner.
Bridge-Wilkinson nearly clinched all three points for the visitors when his shot hit the outside of the post and in injury time the Millers somehow scrambled the ball clear in a hectic goal mouth scramble.
But a winner for Bradford would have been rough justice on Mick Hartford's side, who were worth at least a point.
The result left Harford still seeking his first win at Millmoor after nine games in charge.