Afonso Alves slotted home a 53rd-minute penalty and Gary O'Neil wrapped up victory in injury-time as Middlesbrough deservedly claimed a 2-0 win in the Barclays Premier League points at the Riverside Stadium.
The Brazilian struck after Daniel Sturridge tangled with David Wheater on the edge of the City box and referee Lee Mason pointed to the spot.
O'Neil finished off an injury-time counter-attack but Boro also had keeper Ross Turnbull to thank after fine saves from Vincent Kompany, Stephen Ireland and Shaun Wright-Phillips.
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