The Blues remain in third place with both Manchester clubs ahead of them.
Tiemoue Bakayako trained and will be fit for the weekend game, despite having a minor vehicle crash near the Chelsea training ground on Thursday.
Pedro doubled Chelsea's lead in the 30th when he latched onto Darren Fletcher's misplaced chest pass and drove a fine finish across goalkeeper Jack Butland.
Again Stoke rallied, but Maxim Choupo-Moting was unable to turn a corner home from close range, before Mame Biram Diouf's acrobatic overhead kick flashed wide before the interval.
Conte made a crucial intervention early in the second half to save Marcos Alonso from what appeared to be an inevitable sending off at the bet365 Stadium.
Subs: Afellay (5), Crouch (4).
Cesc Fabregas and Eden Hazard entered the fray fro Pedro and Willian.
It makes Saturday's task look even more daunting for Stoke as they look to bounce back from two successive defeats, a 2-1 loss at Newcastle last weekend and Tuesday's 2-0 Carabao Cup defeat at Bristol City, which Hughes labelled "our worst performance of the season". Costa also contributed to eight goals in his first six games, suggesting that Chelsea have lost nothing of their potency since his departure.
Mark Hughes: "We've made catastrophic errors from the first minute".
"I used to really enjoy watching him play and how he went about his business, because he was different - he had an edge to him and the reaction of other players to him was really interesting. I can not be too disappointed given the circumstances, we had a good go at it but they had too much quality in the end to take it away from us".
It was played from the Chelsea defence by Cesar Azpilicueta and collected by Morata after a simple run between Glen Johnson and Bruno Martins Indi.
Antonio Conte had had enough of Alsonso's lack of concentration on 58 minutes and replaced him with skipper Cahill.
Despite the setback, the Welshman remains confident of taking a point off the reigning English Premier League Champions on Saturday just as they did against Arsenal and Manchester United. "Now it's important to rest well and prepare for another game against Atletico Madrid".
The Spain global was brought in as a replacement for Costa, who was informed by Conte in June that he was free to leave the club and has this this week travelled to Madrid to finalise a return to Atletico Madrid.
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