City's official website confirmed the news that the 41-year-old from Sheldon in the West Midlands will take charge of what is a decisive game in the title race at the Etihad Stadium.
City trail United by three points going into the game but with a superior goal difference, knowing a win would put them in control of their bid to win the title.
Marriner has taken charge of three United games this season, most notably the Premier League encounter with Liverpool at Anfield, after which Patrice Evra levelled his racism allegations.
It will be the first time he has been in charge of a City game this season.
However, he was the official at Old Trafford last season when United beat their Manchester rivals thanks to Wayne Rooney's spectacular overhead kick.
This season his five red cards include one for Blackburn's David Dunn in the infamous Lancashire derby with Wigan at the DW Stadium in November, when he allowed a goal for the visitors to stand after Morten Gamst Pedersen had taken a corner to himself.