The City captain and central defender eased the growing pressure on manager Stuart Pearce as he scored the only goal of a disappointing match.
Dunne, who had previously scored only scored six goals in 227 first-team appearances for City, found the net with a bullet header from a Joey Barton corner.
It was a disappointing night for Boro who had won their previous two Premiership matches as City leapfrogged them in the table.
But it might have been a different story late on as Boro substitute Massimo Maccarone was twice denied by the woodwork.
Pearce wielded the axe following City's 4-0 reverse at Wigan last time out, making five changes.
Summer signings Bernardo Corradi and Dietmar Hamann lost their places as did Matthew Mills, Stephen Jordan and Michael Johnson.
Ben Thatcher received an immediate recall after completing an eight-match ban while Sylvain Distin, Claudio Reyna and DaMarcus Beasley returned after injury and there was a starting spot for Paul Dickov.
Middlesbrough boss Gareth Southgate brought in Robert Huth, Stuart Parnaby and Fabio Rochemback, while Andrew Taylor, Andrew Davies and the injured Mark Viduka dropped out.
Parnaby's appearance proved to be a short one as he limped off after 21 minutes with an ankle injury after being sandwiched by Dickov and Beasley.
Boro had another injury scare when goalkeeper Mark Schwarzer hurt his knee after colliding with Dickov as he raced out of his area to halt a breakaway.
The hosts took the lead midway through the opening period after Georgios Samaras won a corner by forcing Schwarzer to block his angled shot.
And from Barton's corner, Dunne rose at the far post to power home an unstoppable header into the top corner - a sweet moment after he scored in his own net in the defeat at Wigan.
The goal lifted City who went on to carve out a number of other first-half chances, although none troubled Schwarzer.
City had a penalty appeal turned down soon after the re-start when Reyna's shot struck the hand of Huth as he made a desperate block, but referee Howard Webb ruled it was not deliberate.
The second half developed into a niggly affair as six players were booked in a 23-minute spell - Dickov and Barton for City and Emanuel Pogatetz, Huth, Rochemback and George Boateng for the visitors.
Southgate went for broke late on in a bid to find an equaliser as he brought on Italian striker Maccarone and even switched central defender Huth to attack in the closing minutes.
It so nearly reaped dividends as Maccarone twice broke through the City defence only to be denied each time by the frame of the goal with keeper Nicky Weaver beaten on both occasions.