Serbia defender Branislav Ivanovic weighed in with an unlikely double while Didier Drogba scored a penalty on his return to the competition after suspension and injury as Chelsea secured their place in the last 16 with two games to spare.
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It was Anelka, though, who turned the match Chelsea's way after a dire first half had left the Stamford Bridge crowd wondering why they had bothered battling through a city gridlocked by a strike on London's underground tube system.
They came to life four minutes after the restart when Anelka exchanged passes with Salomon Kalou before cleverly beating Andriy Dykan from an acute angle for a typicalyl efficient goal.
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It was his fifth goal in Chelsea's four Group F games - he has scored in all of them - and effectively settled the match.
"Anelka was the key, it was a fantastic goal and the most important goal," Chelsea manager Carlo Ancelotti told reporters.
Drogba's penalty and a header and shot by Ivanovic added the gloss before Nikita Bazhenov came off the bench to stab a late consolation for the visitors.
Chelsea's maximum 12 points guarantees progress and is likely to be enough for top spot even if they fail to get anything from their last two matches.
Spartak and Olympique Marseille, who beat Zilina by a record Champions League away score of 7-0, both have six.
When Ancelotti arrived at Chelsea last year he acted quickly to assure Anelka that he was an important part of his plans and defied received wisdom by regularly pairing him with Drogba.
HAPPY MAN
The Frenchman repaid his faith by scoring three Champions League goals to secure three 1-0 wins and ended the season with 15 in all.
He has 10 already this season and, having retired from international football following the fallout from France's World Cup implosion, shows no sign of slowing.
"He's been the same since I arrived here. Always quiet, calm, works very well. He's happy," Ancelotti said of the 31-year-old.
"He has experience, ability, speed, he's probably in the best period of his career."
Ancelotti said he was not overly concerned by his team's slow start and always felt the game was there for the taking.
"We wanted to start faster but you can't always do it," he said. "In the last 15 minutes of the first half we started giving the ball away a lot and I just asked them to go out in the second half and regain control.
"Anelka's goal was the important one."
Having done the domestic League and FA Cup double last season Ancelotti would obviously love to add the Champions League title and the Italian is well aware of its importance with Chelsea one of three London teams in the competition along with Arsenal and Tottenham Hotspur.
"The final is in London, no London team has ever won it - there is a fantastic motivation," he said.
"But the next step is to win the group. Then we will try to get to the final and then we will try to win it."
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