Henry, it was claimed, suggested it was a policy supported by club management but insisted West Ham United had "nothing against the African race at all".
West Ham on Thursday suspended director of recruitment Tony Henry while the Premier League club investigates allegations that he made racist remarks about African players.
While the Arnautovic's strike boosted his side's hopes of climbing out of the bottom three, it dealt a severe blow to Chelsea's hopes of defending their title.
With Romelu Lukaku scoring his seventh goal in his last six appearances, Manchester United maintained their own blistering form.
West Ham United manager Slaven Bilic has said striker Andy Carroll is nearing full fitness but is not yet ready to start for the club.
Diafra Sakho added to West Ham's striker problems with the news he will miss the English Football League Cup quarter-final with Manchester United.
Jose Mourinho faces disciplinary action from the FA, and a touchline suspension, after being sent to the stands by referee Jon Moss during a 1-1 draw with West Ham.
Manchester United's hopes of Champions League football took a hit on Tuesday in a 3-2 defeat at West Ham that followed an attack on the visiting team's bus as it arrived for the match.
West Ham's Senegalese striker Diafra Sakho has been arrested on suspicion of making death threats and intimidating his former girlfriend, the London police said.
Manchester City and Liverpool endured Premier League frustration on Saturday following Champions League setbacks.