Ronaldo headed in the opener on his return to the starting line-up
Late goals from Nani and Ryan Giggs put Manchester United into the Carling Cup fourth round after Emanuel Pogatetz was sent off at Old Trafford.
United dominated and Cristiano Ronaldo, back for his first start after injury, headed them into a 25th minute lead.
Substitute Adam Johnson volleyed an unlikely second-half equaliser before Pogatetz was given a straight red for a nasty challenge on Rodrigo Possebon.
Veteran Giggs finished coolly and Nani made sure of the win in injury-time.
Playing in front of a 53,000 crowd, United started with a strong line-up which including first-team regulars such as Ronaldo, Nemanja Vidic, Giggs, and Wes Brown, along with youngsters such as 18-year-old goalkeeper Ben Amos and 19-year-old striker Danny Welbeck.
The evening was soured after Pogatetz's 66th minute challenge on Possebon, which left the Brazilian prospect being given lengthy treatment before being stretchered off with a suspected broken leg.
But it was Ronaldo, inevitably, who took centre stage as the match kicked-off after Afonso Alves and Stewart Downing threatened early on for Boro without testing debutant Amos.
The Portuguese put United ahead after 25 minutes with a header from a Giggs corner which bore close resemblance to his goal in the Champions League final against Chelsea in May.
Locally-born Welbeck was in fine form for United while, at 21 and 20 respectively, Nani and Anderson took on responsibility in taking the game to the visitors though Boro's own talented youngster, David Wheater, was instrumental in keeping the deficit to just one going into half-time.
And 12 minutes after the restart as Johnson lashed Boro level when he caught his first-time volley perfectly after Vidic had nodded Downing's cross out of the area.
After Pogatetz's dangerous follow-through cut Possebon down, a nasty gash instantly appearing on the Brazilian's right leg as he yelled in agony before receiving five minutes treatment from United medical staff on the pitch.
Central midfielder Possebon had shone brightly until that point but Giggs got United's deserved breakthrough on 79 minutes, as he chipped home what looked like being a classy winner.
But Nani put a gloss on the scoreline when rounded stranded Jones to slot into an empty net.
Man Utd: Amos, Rafael Da Silva, Vidic, Brown, O'Shea, Nani, Possebon (Gibson 72), Anderson, Giggs (Manucho 84), Welbeck, Ronaldo (Tevez 61).
Subs Not Used: Zieler, Cleverley, Gray, Eckersley.
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