A poignant minute's silence and tribute to the Munich air disaster victims took place before a game which saw Darius Vassell's strike put City ahead.
United became stifled by a staunch City side who extended their lead with a glanced Benjani Mwaruwari header. United struggled overall but got a consolation goal when Michael Carrick shot into the corner in injury time.
The hugely emotive occasion had begun in moving scenes at Old Trafford in respect to the 23 - of which eight were players from the Old Trafford club - who died in the Munich air disaster on 6 February 1958. United's players wore 1958-style sponsorless red shirts numbered one to 11, while City also wore special shirts. United manager Sir Alex Ferguson and counterpart Sven-Goran Eriksson each laid a wreath either side of the centre circle before an impeccably observed minute's silence.
Carrick's consolation strike from 18 yards came too late for United, who were without Wayne Rooney and lost their first game at home in the league this season.
City's win saw them complete the first league double over their arch-rivals for the first time since the 1969/70 season