"It is not the case that both teams have been very aggressive towards the physical side of the game," he told the club's official website. "There were two-footed tackles from Fernando Torres and Didier Drogba and they were sent off, rightly so, but for me theirs were instinctive reactions.
"Of the other red cards, two were for penalties given away when a player was through on the goal and the Bosingwa one was for me dubious and the referee applied the law."
The Blues had Jose Bosingwa and Didier Drogba sent off during the 1-0 loss to QPR last weekend, while Ross Turnbull was given his marching orders during the League Cup victory over Everton in midweek.
Villas-Boas' side was hit with a 20,000 pound fine by the FA on Friday for "failing to ensure their players conducted themselves in an orderly fashion" at Loftus Road on Sunday, although the Portuguese is adamant the Blues have no issues with regards to their discipline.
"We have not lost control and we have not lost discipline," he continued. "My team is not aggressive nor confrontational. We are a correct team and I think that Arsenal is that kind of team as well. It was important to go back to winning ways in the Carling Cup and now it is important for us to go back to winning ways in the Premier League."
John Terry, who has been the subject of FA and police probes as to whether he racially abused QPR defender Anton Ferdinand, is set to feature at Stamford Bridge against the Gunners and Villas-Boas denied he was left out of the trip to Everton as a result of the racism allegation.
"We decided not to take Terry to Everton based on the quality that we have in the squad at centre-back and also based on the fact he had four yellow cards this season," he added. "Frank Lampard was also carrying four yellows into the game. Terry has been excellent in training.
"We have been spreading out minutes played throughout the season so freshness is not a question because we have been able to keep the standard of play going. It is a big, strenuous effort this match coming so soon after a game like the one against Everton but because of this rotation we are completely fresh."
Villas-Boas went on to offer his full backing to striker Fernando Torres, suggesting it will only be a matter of time before the Spaniard starts finding the net on a consistent basis.
"We are speaking about a player who has one goal every two games in all of his career so we are speaking about one of the top goalscorers, so he will go back to goalscoring again. When he finds his confidence he will find the back of the net, I am not worried about that," he concluded.
How do you stay up to date with football when on the move? With http://m.goal.com – your best source for mobile coverage of the beautiful game.