Fernandes was critical of Carrick's tactical approach during the 4-1 defeat to Como, stating that the coaching staff's decision not to press opponents man-to-man as well as sitting back, gave teams too much space and confidence.
When the comments were put to Carrick, he hit back by saying: "If you don't run, and you don't run forward, and you don't run back, you aren't going to win."
Carrick refused to say in his media conference on Friday whether Fernandes would be dropped or if he would be stripped of his captaincy.
However, news broke before United released their team news on Saturday afternoon that Fernandes would be dropped, news that has since been confirmed by the line-up.
Carrick explains his decision
Asked on the choice to drop the club captain, Carrick explained that it was tough but to bounce back from a string of poor results, Fernandes cannot start.
"You've got options to choose from, it's always a difficult decision.
"We've got to make what we feel is the right one for the team to try to get that performance that we want. Pure football (reasons)."
Expanding on his team selection, Carrick added: "Yeah a few changes, it's always a tough decision when you've got choices.
"It's a tough game, they're a very good team and we've got to be at our best to get the result we want. We put a team out there that we feel is capable of doing that."
Fernandes played the full 90 of each of Man United's first seven games of the Premier League season, but he has failed to score or assist in his last five top-flight appearances.
It will be interesting to see how the Red Devils fair without him, as they seek three points against the Cherries at Old Trafford, in front of an impatient home crowd.