The Blues looked to be cruising to a comfortable victory over Manchester United at Stamford Bridge last weekend, when they moved into a 3-0 lead.
However, referee Howard Webb gave what the Chelsea manager viewed as two soft penalties, which Wayne Rooney converted to give the Red Devils hope before substitute Javier Hernandez snatched a point six minutes from time.
In the build-up to the second spot-kick, Villa-Boas felt United striker Danny Welbeck had deliberately tripped over the leg of Blues defender Branislav Ivanovic rather than an intentional foul being committed.
"Referees have pretty clear orders on simulation, but it is difficult for them to assess the difference between simulation and fouls in those situations," the Chelsea manager said.
"They need the right backing to decide on these actions, and when it is simulation a yellow card should be given."
Villas-Boas added: "In the end it is the player who proves his smartness, some are called cheats and divers, others are clever and smart for making the most of the situation, depending on your perspective.
"These are situations that happen in the games. The referee has to have the correct focus, the correct view."
The Chelsea boss insisted: "Ivanovic made the right decision. He was inside the box. was doing everything in his power to avoid contact and Welbeck sticks his leg out to find Ivanovic's leg and the ref gives a penalty for that?"
Villas-Boas believes such incidents should be reviewed and appropriate action taken by Professional Game Match Officials Limited (PGMOL), who oversee the elite full-time top-flight officials.
"Now it is up to (PGMOL general manager) Mike Riley and the governing bodies to decide if the refereeing is up to the right level and [if not] to punish the ref," the Chelsea boss said.
"My view on our last game is that, if a referee is going to award two penalties away from home to the same team, he should be 100% sure they are both penalties.
"Howard Webb was obviously 100% sure in his own mind - my opinion is different, that he was wrong, end of story."