An own goal from opposition substitute goalkeeper Mohd Izham Tarmizi handed the Blues a late win in the first match of their pre-season tour of Asia.
However it was another turgid display under new boss Villas-Boas, who started his reign with a 1-0 win at Portsmouth on Saturday.
“We cannot forget the heat and the conditions, but it is clear that result in the end seems short because we had some good opportunities,” said the Portuguese.
“We are trying to build a new way of playing and things don’t happen in three weeks. That is our target and that is our challenge and hopefully they will happen in the future.”
The occasion was soured by the repeated jeering of Israel midfielder Benayoun by the 85,000-strong crowd. Villas-Boas changed his entire team at half-time and the winner came in the 78th minute, when a free-kick from Didier Drogba (below) hit the post and ricocheted in via Tarmizi.
Villas-Boas added: “Gaining confidence to find the back of the net comes with training and that comes with patience.
“At Chelsea we are prepared to give our forwards this kind of patience because the most important thing for us is to win collectively.
“I will just let things happen naturally.”
Arsenal manager Arsene Wenger is mulling whether to make an improved bid for Phil Jagielka after having a £10m offer for the Everton defender rejected.
Tottenham boss Harry Redknapp has urged unsettled star Luka Modric to be patient and trust Spurs to challenge. Defender Kyle Naughton, meanwhile, has joined Premier League newcomers Norwich City on a season-long loan.
QPR star Adel Taarabt admits he could stay at Loftus Road next season, if his proposed transfer to Paris Saint Germain does not go through.
Manchester City striker Carlos Tevez still wants to leave the club despite the collapse of his move to Corinthians, says his agent Kia Joorabchian.
England winger Ashley Young says his choice to join Manchester United rather than Liverpool was “a no brainer”.
Barcelona have agreed a £23m fee with Udinese for forward Alexis Sanchez. The Chilean will undergo a medical and sign a contract in Catalonia on Monday.