A fortnight after hitting four past play-off hopefuls Brentford, Bradford raced into a two-goal lead against the Cherries.
But Sean O'Driscoll's men dug deep and after clawing their way back to 2-2, midfielder John Spicer had a third ruled out for offside 17 minutes from time.
A minute later veteran striker Windass slotted home his second of the game to edge Bradford back ahead and he wrapped up a thrilling contest with a diving header in injury time.
After an impeccably observed minute's silence to mark the 20th anniversary of the Valley Parade fire disaster, the home side made a determined start, but Jamaican keeper Donovan Ricketts pulled off a vital save at the feet of Bournemouth's leading marksman James Hayter.
The chance was set-up by skipper Steve Fletcher, who was making a club record 424th appearance for the South Coast side, but in City's next attack Windass claimed his own record-breaking strike.
After 19 minutes he was perfectly positioned to volley home Ben Muirhead's flick from just outside the six-yard box and the goal sparked a spell of sustained Bradford pressure.
Seven minutes before the break Bantams midfielder Steven Schumacher took advantage of hesitation in the Cherries back-line to unleash a superb left-foot volley from 25 yards out and keeper Neil Moss had no chance of reaching his spectacular effort.
Bournemouth came out after the interval knowing they had to battle their way back into the contest and their effort was rewarded with two goals in the space of three minutes.
After 60 minutes playmaker Brian Stock drilled a low free-kick past an ineffective Bantams wall and Hayter slid in to guide the ball beyond Ricketts from close range.
The travelling fans were soon celebrating again when centre-half Matthew Mills latched on to Wade Elliott's low right-wing corner to fire a 14-yard drive beyond Ricketts with the aid of a deflection.
At that stage if looked as if the visitors could have claimed a crucial victory, but when Spicer's far-post strike was ruled out, the game swung Bradford's way again.
City looked threatening as the Cherries pressed for the win and Windass showed his quality when he picked up Andy Cooke's intelligent through ball and slid his shot past the stranded Moss after 74 minutes.
That strike took his goal tally to 26 for the season, but he still had one more treat for the home fans as he raced on to Owen Morrison's injury-time cross from the left and beat Moss with a powerful diving header from 12 yards.