Spurs defender Caulker was given a two-match ban and Blackpool winger Ince a one-match suspension after clashes between players and coaching staff at the end of the match in Krusevac in October.
FA general secretary Alex Horne said last month the FA intended to appeal against the bans.
He said then: "It is the FA's vehement belief that its players and staff acted correctly in the face of provocation, including racist abuse and missiles being thrown.
"We are therefore surprised to see that two of our players have been given suspensions.
"We shall await UEFA's reasoning but it is our intention, at this stage, to support our players and appeal these decisions."