Bale picked up his second yellow card in two games for simulation in Tottenham's 3-0 victory at Fulham on Saturday.
Bale, charging at the Cottagers defence at speed, went down under a challenge from Steve Sidwell and referee Chris Foy cautioned the 23-year-old, although replays showed the Fulham midfielder had caught the Welshman's trailing leg.
The former Southampton player received a caution for the same offence on Wednesday after going down following a challenge with Daniel Agger, and again, replays showed there was contact.
Bale's unhappiness at being booked again was clear when he sarcastically applauded Foy for his decision yesterday, and Villas-Boas admits the player is annoyed at gaining a reputation for diving.
"Yes, he is frustrated about it," the Tottenham manager said.
"It is difficult for him, particularly in the last two games.
"If he has a reputation I think it's a little bit unfair... the last two have been unfair.
"I think he uses it as a precaution from different types of challenges. I'm not saying all of the players that challenge Gareth are malicious but the action is so quick that it might look like it's not a foul while it is."
Liverpool manager Brendan Rodgers met with referees' chief Mike Riley earlier this season after he became unhappy with officials' treatment of Luis Suarez, but Villas-Boas has no plans to do the same about Bale.
"No, I don't think so," said Villas-Boas when asked whether he would talk to Riley, head of the Professional Game Match Officials group.
"It's difficult for the referees to judge at that speed."
Bale's afternoon went from bad to worse in the second half as he hobbled off with a hamstring injury after he stretched while shooting at Mark Schwarzer.
The 23-year-old, who has been in top form for the Londoners this season, is expected to be out for two weeks, but Villas-Boas is confident his side will be able to cope without their star winger.
Villas-Boas said: "Gareth is a very important player for us and he definitely will be missed, but it was good to see Clint Dempsey on the left. He changed the range of movements that he does and he got the ball a lot more with more freedom.
"We are fortunate because after Panathinaikos and Everton, the Premier League stops for one week. It will give us time to reassess."
The victory - which came courtesy of a Jermain Defoe double and a rare strike from Sandro - means Villas-Boas' men are now fourth in the Barclays Premier League table.
Fulham, on the other hand, are now going through their worst period of the season.
The west London outfit have not won in their last seven games and have failed to score in their last three.
Manager Martin Jol is refusing to panic, however, and is sure his team will improve when Brede Hangeland and Bryan Ruiz return from suspension and injury respectively.
"We're still only three points away from 20 and there are still three games to go before we've even reached the halfway point of the league programme," Jol said. "Our target is always - like 10 or 12 other teams - to get to 40 points so I'm not worried.
"Hangeland is coming back, Bryan Ruiz is coming back, so hopefully if everyone is on the board we can try to get back on the winning track."
To make matters worse for Jol, he looks likely to lose right-back Sascha Riether for at least two weeks due to a knee injury he suffered on Saturday.
The Dutchman said: "It's the medial ligament in the inside of his leg. It may be not serious. Hopefully it will only be two weeks. If it's a real tear it's eight weeks but I don't think it is."