The struggling Championship outfit put their dismal league run to one side to take a surprising lead against Mourinho’s United.
Dutch forward Marvin Emnes started the clash at Ewood Park brightly and helped the hosts stun United after shrugging off Marcos Rojo and playing through Danny Graham.
Blackburn’s top goalscorer, who had spells at Watford, Swansea City and Sunderland before joining Rovers, steered a superb finish past Sergio Romero to complete a move that even seemed to impress Mourinho.
The Portuguese boss was seen nodding his head and clapping after the 17th-minute goal – although he reacted with even more enthusiasm after Marcus Rashford equalised 10 minutes later.
The England international latched onto a wonderful through ball from Henrikh Mkhitaryan before gliding past stopper Jason Steele and firing home into an empty net.