Earlier in the week Bale had been cautioned when Liverpool's Daniel Agger made minimal contact with him, while on Saturday at Craven Cottage referee Chris Foy decided Bale had dived following a challenge with Fulham midfielder Steve Sidwell, and booked him again.
Villas-Boas defended Bale against claims that he is a diver though, insisting his player was simply protecting himself.
"Gareth is so fast so it is very difficult [for referees] to judge situations," Villas-Boas told reporters after the Fulham game.
"He has suffered big, big injuries to his ankles before and sometimes he wants to protect himself a little bit.
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"He is now very near suspension for two unfair yellow cards and I think you gain a reputation for being a diver unfairly sometimes. This player has suffered a lot in his career.
"It's a little bit harsh on him."
Fulham manager Martin Jol, who was in the opposing dugout, doesn't feel that Bale is a diver either, while team-mate Jermain Defoe said: "I'm not being biased but I think it was a bit harsh to book him.
"When I spoke to him he just said that he was trying to get out of the way."
Bale's day did not get any better late on when he was forced to come off with a hamstring injury that could see him miss some crucial upcoming games for Tottenham. The former Southampton player is expected to be sidelined for up to two weeks.