City's three-match winning streak was halted after a late 2-1 defeat at home to Port Vale.
Despite a dominant second-half showing, Gary Bowyer's men proved unable to make their pressure pay as Vale left West Yorkshire having condemned their hosts to a first league defeat in six.
The visitors started brightly, with both David Worrall and captain Leon Legge going close - inside the opening 10 minutes.
On 18 minutes, their had something to show for their pressure when Richie Bennett laid the dangerous Worrall off who bent into the far corner - from inside the box.
The Bantams were offered a way back into the contest - just before the interval - when Jake Taylor pulled Daniel Devine down, inside the penalty area.
Skipper Vaughan stepped up and made no mistake - sending the ball into Scott Brown’s bottom-left corner to send the two sides into the half-time break level.
City upped the tempo after the restart and went within inches of taking the lead - with 20 minutes remaining.
Neat build up play involving Hope Akpan and Remi Oteh saw the latter pull back for Kelvin Mellor, though his goalbound poke was cleared off the line.
It would be the visitors who had the final laugh, scoring the would-be winner - against the run of play - in the 93rd minute.
After a goalmouth scramble, the ball eventually fell to substitute and former Bantam Will Atkinson who guided it into the top corner.
CITY: Richard O’Donnell; Kelvin Mellor, Anthony O’Connor, Ben Richards-Everton (booked 77'), Connor Wood; Callum Cooke, Hope Akpan, Daniel Devine (Paudie O’Connor 90+4'); Zeli Ismail, James Vaughan, Aramide Oteh (booked 56'). Subs (not used): George Sykes-Kenworthy (GK), Reece Staunton, Adam Henley, Jermaine Anderson, Shay McCartan, Omari Patrick.
GOALS: Vaughan (45+1’ pen).
PORT VALE: Scott Brown; James Gibbons, Leon Legge (c), Nathan Smith, Cristian Montano; David Amoo, Scott Burgess (Will Atkinson 73'), Luke Joyce, Jake Taylor (booked 45’, Shaun Brisley (90+5'), David Worrall (booked 65'); Richie Bennett. Subs (not used): Jonny Maddison (GK), Jordan Archer, Callum Evans, Rhys Browne, Tom Pope.
GOALS: Worrall (18’), Atkinson (90+3').
ATTENDANCE: 13,345 (245 visitors).
REFEREE: Graham Salisbury (Lancashire).