Caulker will miss the England Under-21 team's Euro 2013 games against Italy and Norway after UEFA found him guilty of improper conduct for his actions during a post-match brawl against Serbia in October.
European football's governing body have been criticised for banning Caulker and his team-mate Thomas Ince, and for fining the Serbian FA £65,000 - some £15,000 less than was handed out to Nicklas Bendtner for revealing a sponsor's logo on his underpants during Euro 2012.
The Tottenham manager concedes that his defender is extremely unhappy with UEFA's action against him.
"I spoke to the player and he is obviously very disappointed," Villas-Boas told a press conference.
"It is difficult to take after (what) I heard from my players - from Danny [Rose], from Steven, from Adam Smith - from the situation they went through to see that the outcome is this one.
"I imagine the FA will appeal. I think they are entitled to do it. They have shown disappointment with the decision and I think they are going to take it forward in various different ways which I think should include trying to put right what is wrong in Steven's sanction."