On the day of his 29th birthday, Contador broke away to win the race, which took place over ten laps of a 2.8km circuit in the city's Old Town, and was dubbed the Tour de Jerusalem by local organisers.
Contador and the Saxo Bank team are currently in Israel on a team-building camp ahead of the 2012 season.
The Spaniard will find out in the New Year if he is to face a ban of up to two years from the Court of Arbitration for Sport for testing positive for clenbuterol in the 2010 Tour de France.
He was cleared by the Spanish Cycling Federation, but the World Anti-Doping Agency (WADA) and the International Cycling Union (UCI) both appealed that decision.