Steve Morison scored the 85th minute winner to send the Lions, who missed out to Barnsley in last year's playoff final, back to the Championship after two seasons in the third tier.
The South-East Londoners, who ended the season in sixth place and six points behind Bradford, join already promoted Sheffield United and Bolton Wanderers in going up.
The pitch invasion by Millwall fans angered Bradford manager Stuart McCall, who told Sky Sports that he was "close to clocking one or two of them".
(Reporting by Alan Baldwin, editing by Pritha Sarkar)
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