Chelsea manager Antonio Conte made seven changes from his side's win over Manchester United at the weekend, and saw his team fall behind to Cheikhou Kouyate's superb 11th-minute header.
Chelsea boss Conte defends touchline 'passion'
Edimilson Fernandes added a second early in the second half and although Gary Cahill reduced the arrears in stoppage time, after substitute Eden Hazard had hit the post, it came too late.
There was a heavy police presence inside and outside the former Olympic Stadium, where there has been trouble involving West Ham fans in previous games.
But rival supporters clashed at the end of the game, with some throwing chairs and bottles.
Mourinho, Conte keep mum over touchline spat
"I noticed it, but I wasn't watching it so I really don't know what happened," said West Ham manager Slaven Bilic. "The game was on. Whatever happened, it's a shame and as a club and a team we are totally against it, of course."
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