Chelsea have now lost half of their opening 10 fixtures in defence of the title they won in May after a first-half implosion at Upton Park, when Mourinho was sent to the stands at half-time.
Mourinho, who is appealing against a Â£50,000 fine and suspended one-match stadium ban for comments made about officials following the October 3 loss to Southampton, can expect further disciplinary action.
The Blues issued the first managerial vote of confidence in Abramovich's 12-year ownership in the wake of the Southampton defeat and there is no sign of a dramatic change of heart - yet.
The 52-year-old Portuguese faces a fierce test of his credentials in the next 10 days, with Chelsea travelling to Stoke at the start of the defence of the Capital One Cup on Tuesday night.
Next is the visit of Jurgen Klopp's Liverpool in the Barclays Premier League, before another tricky Stamford Bridge contest against Dynamo Kiev, one of two sides above Chelsea in Champions League Group G.
The three matches could kick-start Chelsea's season, or see Mourinho depart after a campaign which has lurched from one storm to the next.
Mourinho first must await the submission of referee Jonathan Moss' report, which the FA will receive by Monday, into a fractious finale to a first half in which West Ham were largely on top.
After Mauro Zarate's opening goal, Chelsea felt a succession of decisions went against them.
Kurt Zouma had a header cleared off the line, with only goalline technology proving no goal had been scored, before Nemanja Matic was booked for hauling down Cheikhou Kouyate as he led the counter attack.
Next Cesc Fabregas thought he had scored from Willian's pass, only to be adjudged offside.
It was a decision which infuriated Mourinho, who made his displeasure known to the fourth official and assistant referee.
Matic was then shown a second yellow card for a touchline foul on Diafra Sakho
It was an unnecessary challenge in the circumstances as defenders were covering.
Silvino Louro, one of Mourinho's assistants, was apoplectic and sent to the stands.
When Mourinho did not emerge on the touchline for the second half, instead being found in the West Ham directors' box, it became apparent that he, too, had been dismissed at the interval.
West Ham appeared more distracted than Chelsea, who looked better with 10 men, and Gary Cahill equalised only for Andy Carroll to head in a deserved winner for the Hammers.
Mourinho did not speak to the media, in breach of Premier League regulations.
But the likely fine is the least of his worries, with the FA awaiting Moss' report.
It is not expected to automatically trigger the stadium ban, as that sanction, which is subject of an appeal, appears to relate specifically to rule E3 and improper conduct surrounding comments on officials.
Further disciplinary action awaits for Mourinho, though, while Chelsea can also anticipate a fine for having more than five players yellow carded in the game
Seven cautions were issued against them.
Cahill, who spoke to the broadcast rights' holders, felt the fine margins went against Chelsea, illustrating their season in microcosm.
He told Chelsea TV: "It's a summary of our season sometimes.
"You're talking about the smallest of margins
At this moment in time they're going against us, not for us.
"What do you do? Do you sit back and feel sorry for yourselves? Of course you don't.
"You need to keep going
You pick yourselves up and go again, work even harder to make this turnaround and the good times will feel even better.
"When you have a result like this you want to play again tomorrow
It's better that games are coming thick and fast."
Source : PA