The 26-year-old began the season with the captain's armband but manager Derek McInnes handed the responsibility to midfielder Skuse following his return from injury.
Skuse has now captained the club in their last three games and McInnes explained his decision to change his skipper.
McInnes told the Bristol Evening Post: "I just feel Liam Fontaine needs to concentrate on himself a wee bit.
"He needs all the support he can get from everybody. It is too easy to just criticise and all the rest of it.
"We felt maybe taking the captaincy off him would allow him to concentrate on his own game. Taking the captaincy away does not detract from him as a player.
"He is a very capable centre-back and we felt a little less responsibility might just help him.
"Cole Skuse has always been a key player for me and will play week in and week out for me, because of what I think of him. I think he was a natural choice and we need as many captains on the pitch as possible."