The visitors' experienced goalkeeper Timo Hildebrand paid the price for dwelling on the ball in the first half when his belated attempt at a clearance hit Samuel Eto’o and cannoned into the back of the net.
Eto’o was the scourge of the Schalke keeper once again after the break, converting only his third goal for Chelsea, and his replacement Demba Ba scored his first of the season to ensure Jose Mourinho's men moved clear at the top of Group E.
Chelsea have now won all three of their Champions League games since losing the campaign's opening fixture against Basel and this was their 100th victory in UEFA competitions.
Schalke, by contrast, suffered a first defeat in eight away games, but remain second in the group and still in with a good chance of repeating last season’s achievement of reaching the knockout stages.
Eden Hazard was not even on the bench for the clash and Eto'o replaced the injured Fernando Torres (thigh) as Chelsea boss Jose Mourinho reacted to Saturday's 2-0 defeat at Newcastle by making six changes to his starting line-up.
Schalke manager Jens Keller opted for the experience of Jermaine Jones in midfield over teenager Max Meyer and striker Adam Szalai was passed fit despite requiring an ear operation after Saturday's win at Hertha Berlin.
Mourinho was baffled by his side's display at Newcastle and will likely have been scratching his head again in the first five minutes as Schalke spurned two opportunities.
Petr Cech could only watch on as Julian Draxler's right-foot strike flashed just past the far post and the Germany midfielder then set off on an incisive run before setting up Szalai, who also fired narrowly wide.
Chelsea started to get into their stride and Hildebrand gifted them the lead after 31 minutes as Eto'o charged down the 34-year-old's clearance.
The lively Draxler came close once again early in the second period when he cut in from the right and lined up a measured left-foot strike, but Cech made a fine fingertip save.
the hosts doubled their lead nine minutes into the half as Willian surged forward and played in Eto'o. The former Barcelona striker beat Hildebrand with a clinical right-foot finish across goal.
Ba then got in on the act when Frank Lampard set him up for a well taken left-foot volley seven minutes from time.