And while Wenger was fuming, Chelsea manager Andre Villas-Boas declared his team was back in the title race following a last-gasp 2-1 victory over Wolves.
Arsenal took the lead over Fulham through Laurent Koscielny but were forced to play the closing stages with 10 men after Johan Djourou’s dismissal, with Fulham taking advantage through goals from Steve Sidwell, a former Gunners midfielder, and Bobby Zamora in the final five minutes.
“The referee influenced the game completely the wrong way in my opinion,” said Wenger after a defeat which dropped his side into fifth place in the table.
“We cannot influence that … in the last 10 minutes, we lost the game because we were down to 10 men.”
Arsenal could have secured the points well before the late drama if Probert had awarded a penalty for Philippe Senderos’s trip on Gervinho in the 13th minute.
“I am surprised,” Wenger said. “You want the right decision.”
He added: “We had a penalty in the last game (against QPR), a clear handball. We had a penalty at Man City, we had a penalty at Villa Park.
Swiss defender Djourou’s first booking was for a slide on Mousa Dembele and his second, which led to an automatic dismissal, came when he fouled Zamora.
“The first yellow card was not a yellow card, the second yellow card was a foul for us,” Wenger said. “It was 100 per cent a penalty for us in the first half.
“It was bad for us, the fact we didn’t take our chances in the first half and it made the difference.”
Djourou’s suspension gives Wenger another headache as Bacary Sagna, Carl Jenkinson, Kieran Gibbs, Andre Santos and Thomas Vermaelen are all injured, leaving Arsenal short of full-backs.
“He has done well, we are short, we have lost three left-backs and two right-backs. What can you do? You cannot buy 10 full-backs,” Wenger said.
Zamora’s goal came after he’d struggled with injuries and amid reports of a decline in his relationship with Fulham manager Martin Jol.
“A lot of it has been blown well out of proportion,” Zamora said, playing down talk of a rift. “I’m looking forward to playing, doing well and hopefully scoring a few goals.”
Meanwhile, Frank Lampard’s dramatic 89th-minute goal eased the pressure on Villas-Boas as Chelsea ended a four-game winless streak at Molineux.
Although still eight points off top spot having played a match more than the two Manchester clubs, Villas-Boas backtracked on his previous suggestion his team are out of the title reckoning following a weekend of shocks at the summit.
“If we go on a winning streak of five or six games, which we are capable of, we can still be fighting for this league,” Villas-Boas said.
Elsewhere, Blackburn were brought down to earth following their away win over Manchester United at the weekend, suffering a 2-1 defeat to Stoke at Ewood Park as Peter Crouch scored twice for the visitors.
Aston Villa’s feelgood factor from their win at Chelsea was also shattered, with newly-promoted Swansea scoring a 2-0 win at Villa Park.
And QPR captain Joey Barton was hero and villain at Loftus Road as Rangers crashed to a 2-1 loss to Norwich, a defeat that edged Neil Warnock’s side ever closer to the relegation zone.
Barton shot Rangers ahead on 11 minutes, drilling in a low finish from Clint Hill’s cross.
But Barton’s joy turned to despair on 36 minutes, when the midfielder was controversially sent off for an apparent headbutt in a confrontation with Bradley Johnson.
