Unlike rivals Arsenal and Liverpool, who handed the Malaysian national side a firm beating, Chelsea struggled to break down a stubborn Malaysian Selection side made up of mostly Olympic Under-23 players.
It took a controversial goal by Didier Drogba in the 80th minute, from a free-kick, as the London side belatedly broke the deadlock at the Bukit Jalil National Stadium in Malaysia's capital Kuala Lumpur.
However, replays showed that the ball, which hit the post before bouncing off Malaysian goalie Mohamad Izham Tarmizi?s back, did not cross the line.
Malaysia then had a glorious opportunity to equalise in the 85th minute, but A. Thamil Arasu saved Chelsea's blushes as he shot wide after being put through with only the goalkeeper to beat.
Villas-Boas admitted his side should have scored more with the chances they created and praised Malaysian goalkeeper Mohamad Farizal Marlias? performance.
"The Malaysian keeper did well to limit the number of goals, and they had two good chances to equalise on the last stretch of the match," Villas-Boas said.
"We lacked vertical passes, and we played horizontally most of the match. We created enough chances to score but failed to hit the target," he added.
The sour point of the match, however, was the constant booing of Benayoun -- the first Israeli to play in Malaysia -- in the first-half.
Muslim-majority Malaysia is an ardent supporter of the Palestinians and has no diplomatic relations with Israel.
That aside, the match was a dull affair with the sides rarely creating chances.
With 10 minutes gone a mix-up in the Malaysian defence allowed Frank Lampard, who wore the captain?s armband, a free shot but he blasted wide.
Chelsea were then denied two more chances when last-ditch tackles from Malaysian centerback S. Subramaniam thwarted the danger from first Salomon Kalou and then Fernando Torres.
In the 42nd minute, Lampard had the best chance of the game after Kalou sliced open the Malaysian defence with a wonderful pass but the veteran Chelsea midfielder failed to connect with the ball.
On the stroke of half-time, Benayoun failed to silence the abuse from the crowd when he mis-kicked in front of the goal.
Villas-Boas kept to his word and replaced his entire starting 11 at the break, bringing on captain John Terry, Drogba, Nicolas Anelka and Daniel Sturridge.
Yet it made little difference until Drogba's late -- and lucky -- intervention.
Malaysian coach Ong Kim Swee said the team accepted Drogba's goal though it was "quite dubious".
"We did well despite the result... The 0-0 scoreline in the first half gave the boys the impetus to do better in the second half," he said.
"This match will be a good exposure and experience before the third round of 2012 Olympic qualifiers," he said.
The Stamford Bridge club will next go to neighbouring Thailand for a match with the Thailand All Stars. They then head to Hong Kong, where they play a friendly against Kitchee, a local team.
Arsenal beat Malaysia 4-0 on July 13 and Liverpool beat Malaysia 6-3 on Saturday in friendlies at the same stadium.
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