Eddie Nketiah salvaged a point at Emirates Stadium after Arsenal initially went 1-0 down to Fulham through Josh Maja.
Nketiah scored his second goal of the season in the Premier League after a late equaliser in the North London sun.
There will be continued VAR controversy after Gabriel brought down Mario Lemina in the box before Fulham scored the opener.
The Gunners could potentially drop in to the bottom half of the Premier League table if results do not go their way regarding Aston Villa and Leeds United.
A truly miserable season for Mikel Arteta, who must salvage glory in the Europa League to gain European football next season.
Story of the match
Gabriel Martinelli and Alexandre Lacazette almost combined to break the deadlock inside two minutes.
The number 35 connected with a bouncing ball in the penalty area but his attempted loop drifted wide. A bright start.
It was the side from West London who provided the first highlight of the game. A deflected Bobby Reid effort landed at the feet of Maja, who couldn't rearrange his feet in time to land a clean connection.
The ball trickled past the far post, leaving the Fulham camp with hands on their heads. A superb chance to take the lead.
The Clock End struck 14:00 and there was not much to talk about thus far. Fulham were playing with confidence, trying to be expansive and play from the backline.
Arsenal were relying on the counterattack with Martinelli and co on the flanks. The football was too pretty without a penetrative finish.
Dani Ceballos thought he scored his first Premier League goal for Arsenal after his lofted header looped over Alphonse Areola.
He wasn't left celebrating long after VAR erased the goal due to Bukayo Saka's toe being in an offside position.
Moments later a second goal was chalked offside. This time there was no VAR needed after Emile Smith Rowe failed to beat the trap in the build up.
Martinelli delivered a low cross which ricocheted off Joachim Andersen before bulging the net. Another let-off for Scott Parker.
Arteta's men came steaming out of the blocks in the latter half. Lacazette looked at the heavens after dragging a shot wide from around 25 yards. He will be disappointed to have not tested Areola.
The hour mark brought the first real talking point after VAR decided on a penalty for Fulham. Gabriel brought down Lemina in the box to win the spot kick.
Maja made no mistake with the penalty after he dispatched with severe confidence. Fulham had a precious lead to hold onto.
The introduction of Nicolas Pepe meant Arsenal had more firepower and creativity in the final third.
His presence was noticed almost instantly after he forced a superb save from Areola via a header at the far post.
Nketiah entered proceedings in replace of Lacazette after 70 minutes. Arteta was left frustrated after the Hale End graduate saw a chance go begging in front of goal.
Another occasion when Arsenal should have tested Areola.
A flurry of Gooner attacks mounted for nothing, even after an additional seven minutes at the end of the game.
At the death, Nketiah poked home an equaliser after Fulham failed to hold on. The ball was fired across the face of goal and there was Nketiah, who shown the traits of a clinical poacher.
The league campaign is dead in the water after being loomed in mid-table all season.
The priority for Arsenal is the Europa League. A tie with Unai Emery and Villarreal awaits in the semi-final. An extra incentive to beat the man who surpassed Arsene Wenger at Emirates Stadium in May 2018.
Every player is playing for selection in the European competition. Due to the heavy rotation against The Cottages, it's clear that Arteta is experimenting with his squad.
Mid-table sides usually start to tail off at this part of the season. There is no room for complacency in the dressing room with the potential of Champions League football a possibility.