The 32-year-old will oversee the encounter between the Premier League's top two sides, with Gary Beswick and Simon Bennett his assistants and Jonathan Moss the fourth official.
Mourinho described him as "a referee with fantastic potential" but felt aggrieved after his midfielder was given two quick yellow cards in the 1-0 loss at Stamford Bridge.
He was also frustrated Oliver had awarded penalties against United in three Premier League matches in which they dropped points: in a 3-1 loss to Watford and 1-1 draws away to Everton and at home to Liverpool.
Oliver was in charge of the derby at the Etihad Stadium in 2014, when he sent off Chris Smalling for two yellow cards, and in United's 1-0 win at City in March last year, after which he was criticised for not giving a penalty to the visitors for a Martin Demichelis challenge on Marcus Rashford.
Meanwhile, Craig Pawson will referee the Merseyside derby between Liverpool and Everton at Anfield.