The Blues went behind to an early Shane Long goal before Villas-Boas elected to bring on Malouda in place of Salomon Kalou after just 30 minutes.
It proved a match-winning move as the Frenchman scored the winner seven minutes from the end after Nicolas Anelka had netted a second-half equaliser.
Malouda hailed the move of his Portuguese boss, telling ESPN: "I think we had to change something in the first half.
"The manager put me in and I tried to make chances with more crosses.
"The manager made a few substitutions.
"We are glad that it worked. It's nothing new and I think it will remain like this until the end of the season.
"There is a lot of competition in this squad. Everyone is under pressure."
Asked what Villas-Boas told his side at half-time, he replied: "He asked if we were willing to show other clubs we are a championship contender. Are we ready to change things?
"It was a simple message. We had to take more risks and play with more character."