A hard-fought encounter at the DW Stadium finished with the spoils shared, after Daniel Sturridge's second-half opener was cancelled out by a close-range Jordi Gomez strike with just three minutes left on the clock.
"The first 20 minutes of the second half were good," said Villas-Boas. "We had to be patient to get the goal and once we'd scored we could have maybe pushed on for another but we decided to hold on and try to exploit the spaces in behind.
"We conceded three minutes from the end and that's the disappointing thing because we expected to win the game.
"It's a pity, the players fought hard but confidence isn't affected. We have to see how results go tomorrow to see where we stand."
Chelsea went into yesterday's game off the back of three consecutive victories in the Barclays Premier League, and Villas-Boas explained that a successful squad doesn't suddenly turn into a bad group of players on the basis of a solitary result.
The Blues showed in glimpses yesterday the attacking threat that they do pose, when the Portuguese tactician made half-time changes to liven up what had been a sterile first-half display.
"Romeu came off at half time because I felt we lacked a bit of creativity," he continued. "We introduced another winger and allowed [Juan] Mata to play in between the lines.
"We tried hard, it was difficult because Wigan are a different side now. They have momentum from their recent run of good results, the crowd were behind them and they fought hard to get the points.
"They made the best of our lack of concentration. We had [Jose] Bosingwa, [John] Terry and [Ashley] Cole behind the ball but it was part of a situation where [Petr] Cech lost track of the opponent and they scored."