Earlier this month, Fernandes publicly questioned Carrick's tactics following United's 4-1 Champions League defeat to Como as he suggested his team didn't press well enough against the Serie A side.
He argued that allowing Como too much possession gave them confidence and forced United to expend energy chasing the ball, drawing criticism from several pundits including club legend Wayne Rooney, who labelled him a baby.
As a punishment, Carrick has decided to punish his captain by removing him from the starting XI for the clash against Bournemouth this afternoon.
United were reported to have decided against fining him but did not rule out stripping him of the captain's armband after his public outburst.
The Red Devils have won just one of their opening seven league games and begin the weekend languishing in 15th place. A win is imperative for Carrick and removing Fernandes from his starting line up could also take away creativity in a midfield lacking a spark.
Further punishment could be imposed on Fernandes following the Bournemouth clash, and it is yet to be seen who could replace the Portuguese international if he is stripped of his captaincy.