Two goals in two minutes settled the game with Vasili Berezutskiy making the breakthrough in the 50th minute after converting a cross from the right, and Alexander Kokorin doubling the lead in the 52nd minute with a rising shot from the edge of the penalty area.
Denis Glushakov made it 3-0 16 minutes from time when he reacted first to a penalty from Roman Shirokov that rebounded back off a post.
Eran Zehavi, guilty of the handball that led to the spotkick, headed a consolation for Israel in stoppage time.
Russia coach Fabio Capello told reporters: “We started the second half very aggressively, we pressed them well, we immediately covered them, managed to steal the ball on their side of the field.
Capello, famously hard to please, was not entirely happy though.
He continued: “I don’t like it when my team lets in goals though and I don’t like it when it happens in the last minute of a game.
“Probably it speaks of letting yourself off your guard. But in general, besides this mistake, I liked how our defenders played.”
Defeat in St Petersburg effectively ended Israel’s hopes of finishing in the top two and claiming a playoff place and their long wait for a second World Cup finals appearance since their only one in 1970 will go on.
Russia top the group with 18 points from eight matches, one point more than Portugal. Israel are now a distant third with 12 points from their seven matches.
If Russia win their last two qualifiers in Luxembourg and Azerbaijan next month they will reach the finals, although Portugal, with home matches to come against Israel and Luxembourg, are ready to pounce if they make any mistakes.
(Reporting By Thomas Grove in Moscow, editing by Mike Collett)