After a goalless first half, Boro were again failing to find their feet in front of goal, something which has dogged their recent performances.
Steve McClaren's side, though, proved too strong and produced a dominant second half display to take all three points.
Boro took the lead after 53 minutes when England defender Ugo Ehiogu rose to head home a Geremi cross.
The Teessiders then doubled their lead less than 10 minutes later when Alen Boksic rose to head his first goal of the season after Geremi crossed once again.
City then pulled themselves back into the game after they took advantage of a poor Tony Vidmar clearance when Nicolas Anelka just managed to beat Mark Schwarzer in the home goal.
Kevin Keegan's side then saw their hopes hampered when Shaun Wright-Phillips received a second yellow card for a challenge on Jonathan Greening.
Boro took advantage of playing ten men as Cameroonian star Geremi managed to get his name on the score-sheet with just minutes left as he collected a rebound from a Massimo Maccarone effort to rifle home.
