Tottenham defender Caulker was given a two-match ban and Blackpool attacker Ince banned for one game after home fans in Krusevac targeted England players including Danny Rose with racist chanting.
The duo will presently miss the start of England's final campaign in Israel this summer, while Rose's one-match ban for the red card he received following his explosive reaction will stand regardless.
England won the match 1-0 to secure a 2-0 victory on aggregate.
In December, FA general secretary Alex Horne said: "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."
The Serbian FA was ordered to play one U21 game behind closed doors and fined £65,000 by UEFA's disciplinary panel.
UEFA president Michel Platini is concerned that the punishment meted out to Serbia was not harsh enough and is considering an appeal against the panel's decision.