Felix became the first Chelsea player to see red on his Premier League debut for the club when he was dismissed for a reckless challenge on Fulham’s Kenny Tete.
Chelsea had battled back from 1-0 down to level the match at Craven Cottage but Felix’s departure gave Fulham the boost they needed to go on and clinch the three points.
Ex-Chelsea star Willian gave Fulham a first-half lead before Kalidou Koulibaly scrambled home an equaliser shortly after the interval.
Fulham took control of the Premier League fixture following Felix’s dismissal and Carlos Vinicius headed home a winner with 20 minutes remaining.
It was a dramatic and unfortunate end to Felix’s Chelsea debut, with the Portugal forward arriving at Stamford Bridge on a loan move from Atletico Madrid earlier in the week.
‘It sums up where we are at the moment – everything that can go wrong, is going wrong,’ Potter said after Chelsea’s 2-1 west London derby defeat.
‘It was a forward’s tackle from Joao, there was no malice in it but I understand why it was a red. It is another blow the hits keep coming at the moment.
‘He was really good you could see his quality in the game so it is doubly disappointing for us because he was looking dangerous throughout.
‘I don’t think there was too much malice in it and it is an unfortunate action and we are going to lose him now for three games.’
Chelsea have now won just two of their last 10 matches in all competitions, slipping to 10th in the Premier League.
‘As you can imagine, the dressing room is disappointed,’ Potter added. ‘We are in a bad moment, a bad run.
‘We came here with the ambition to win, we haven’t done it. We feel for the supporters, we are upset. We have to recover.’
To make matters worse for Chelsea, they are now sweating over the fitness of summer signing Denis Zakaria, who hobbled off in the second half.
Chelsea are already without full-backs Reece James and Ben Chilwell, midfielders N’Golo Kante and Jorginho, wingers Raheem Sterling and Christian Pulisic, striker Armando Broja and £70m summer signing Wesley Fofana.
Asked for an update on Zakaria, Potter said: ‘The only assessment right now is that the problem is at the top of his quad.
‘He felt it when he cleared the ball. In terms of the extent, it’s too early to say. We will see how he is over the next 24 hours.’
Chelsea face London rivals Crystal Palace on Sunday and could be in the bottom-half of the table by the time Patrick Vieira’s Eagles visit Stamford Bridge.
Fulham, meanwhile, climbed to sixth in the Premier League after securing only their fourth win against Chelsea in 53 top-flight matches.
The Cottagers had gone 20 Premier League games without a win against Chelsea, a run stretching back to March 2006.
Fulham boss Marco Silva said: ‘Chelsea is a super team, they are a massive club and their budget is completely different to ours, you can’t compare.
‘It was a great night for our fans and they deserved it. For our football club, for our fans it’s special and I definitely felt it at the final whistle – the way they celebrated was a really important moment.
‘Our players have been brilliant for the season so far but we know we are just in the middle of the season and as a manager there’s big room to improve.’
MORE : Graham Potter avoids Kepa criticism after Chelsea’s defeat to Fulham
MORE : Fulham delete tweet mocking Joao Felix after red card in Chelsea loss
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