United dominated the game but only had John O'Shea's 18th-minute goal to show for their efforts.
"John O'Shea's injury complicates the fact we need a new partner for Gary against Turkey, " said Kerr.
It follows the news that defenders John O'Shea and Jonny Evans have been ruled out of action until January.
Paul Scholes gave United a first-half lead, with John O'Shea and Kieran Richardson were on target after the break.
BBC: SPORT | Football | Europe | Ferguson salutes maturing Man Utd
City Affair, trained by John O'Shea, was unruly before the start of a novices' selling hurdle and unseated O'Neill.
BBC: SPORT | Other Sport... | Horse Racing | Probe into jockey 'butt' on horse
And late on United might have concede a penalty when Dong-Gook Lee went down following a John O'Shea tackle.
BBC: SPORT | Football | Premiership | Man Utd 1-1 Middlesbrough
The versatile John O'Shea will partner Nemanja Vidic in central defense if neither Ferdinand nor Evans is fit to play.
The equalizer came in the 51st minute as John O'Shea's cross from the right was met by Berbatov's spectacular overhead kick.
This will stretch a defence that is already without injured quartet Rio Ferdinand, Nemanja Vidic, Rafael da Silva and John O'Shea.
Having reviewed a video of the incident at Stratford involving the John O'Shea-trained gelding, the HRA disciplinary panel is set to hold an inquiry on 3 August.
BBC: SPORT | Other Sport... | Horse Racing | O'Neill sorry for butting horse
Ferguson made a triple substitution in the 61st minute, sending on Owen Hargreaves, Anderson and John O'Shea for Patrice Evra, Michael Carrick and Ferdinand.
Then Eto'o played a dangerous ball across the United area and Messi appealed for a penalty after appearing to be pulled back by John O'Shea.
When John O'Shea jabbed the ball into the danger area following Nani's corner, Berbatov was clearly in an offside position as he flicked a finish beyond Boruc.
Vidic had to be alert to scramble clear after James Milner beat John O'Shea and crossed but in the end neither side could breach the other's back four.
United suffered two more injuries in the first half when Nemanja Vidic and John O'Shea had to go off, two substitutions that disrupted the champions' impressive early rhythm.
Sir Alex Ferguson made a tactical switch after 66 minutes, replacing Saha with John O'Shea, who was pushed into a protective role in front of the back four.
BBC: Wayne Rooney celebrates putting Man Utd ahead in the derby
John O'Shea and Park Ji-Sung both had good opportunities blocked in the box, while Zenit keeper Vyacheslav Malafeev did well to deny Rooney with the minutes ticking down.
The Rams led 1-0 from the first leg but a fierce Nani strike levelled the tie and defensive errors let John O'Shea and Carlos Tevez put United in charge.
Dunne directed a free header after a Duff corner to the unmarked John O'Shea but the Manchester United defender skied his effort before the French earned a relieving free-kick.
His list of injured defenders includes England internationals Gary Neville and Wes Brown, who both limped out of Saturday's game, plus longer-term defensive casualties Rio Ferdinand, John O'Shea and Jonny Evans.
Evans will now be suspended for three games, putting further pressure on a United defence that is already without injured quartet Rio Ferdinand, Nemanja Vidic, Rafael Da Silva and John O'Shea.
Robert Green then made a superb fingertip save to deny John O'Shea at the other end before Rooney screwed his volley wide after Heinze picked him out with a superb far-post cross.
Stoke dug in and a trademark long throw from Rory Delap was headed towards his own goal by John O'Shea, only for Edwin van der Saar to claw the goalbound ball to safety.
John O'Shea fashioned the original opening with a perfect pass inside Anelka and Giggs was equally incisive with a cross that was bundled into the roof of the net in trademark fashion by the predatory Hernandez.
John O'Shea, the 57-year-old former general manager of the Texas unit of ABB, was arrested last week for his alleged role in a conspiracy to bribe Mexican government officials and get business from the Comision Federal de Electricidad, or CFE.
Smalling is a real talent in the making, but he is inexperienced and, with Rio Ferdinand still out, you could now be looking at a United back four of Patrice Evra (if he's fit), Smalling, Wes Brown and John O'Shea.
John O'Shea of Irish charity Goal told the Guardian newspaper he could not allow aid workers to move into Haiti from the Dominican Republican because he had "no guarantee that the people driving them are not going to be macheted to death on the way down".
Knighthoods are also conferred on Professor Timothy O'Shea and Professor John Savill, both of Edinburgh University, for services to higher education and clinical science respectively.
应用推荐