David Moyes revealed after the 1-0 Capital One Cup triumph that Cleverley was in his plans to play alongside Ryan Giggs in the engine room after impressing when coming on during the derby-day defeat to Manchester City.
However, Cleverley's absence allowed Jones to display his versatility with a typically all-action performance containing some crunching tackles.
"We lost Cleverley with an injury in training and it left me a little bit short of midfield players," said Moyes. "Michael Carrick has played [a lot] and Marouane Fellaini was cup-tied so we were short of bodies.
"I wasn’t sure if I wanted to play Phil in midfield but I felt he played very well. He broke the game up for us at the right time and we tried to get him in the middle of the pitch as much as we could."