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.
The Tottenham manager said: "I spoke to the player and he is obviously very disappointed. 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."
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.
Villas-Boas added: "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."
Villas-Boas has included Caulker in his squad for Sunday's home game against Swansea. The Spurs boss revealed good news from the treatment room on Friday, declaring that Gareth Bale, Michael Dawson, Scott Parker and Benoit Assou-Ekotto all have a chance of playing against the Welshman.
Bale has been absent since suffering a hamstring injury against Fulham two weeks ago, a match where he earned his fourth yellow card of 2012 for simulation. Villas-Boas reckons the Welshman's tag as a diver is unfair, and he said as much to referee Andre Marriner when he visited the club's training ground last Tuesday in a pre-planned visit.
"We received the visit of the referee this past week," Villas-Boas said. "Gareth and I spoke with the referee about this situation.
"Gareth has gone through a difficult time in his career. He has had potentially-career threatening injuries and sometimes for the pace that he goes at it looks like a dive from the player when he is actually protecting himself.
"It's a tag that if he has gained it is unfair. But it doesn't bother him in any way shape or form."
- Sports & Recreation
- Gareth Bale