Mikel Arteta faces an anxious wait over the fitness of four defenders ahead of next week's Champions League quarter-final first leg against Real Madrid.
The Gunners were boosted by the return of Bukayo Saka, who scored only seven minutes into his Arsenal comeback, but they lost Gabriel Magalhaes to an apparent hamstring injury.
The Brazilian defender was substituted just 16 minutes into the game after pulling up while sprinting back towards his own goal. The centre-back was seen grimacing as he laid on the turf clutching the back of his right leg, and was subsequently replaced by Jakub Kiwior.
Meanwhile, Jurrien Timber was forced off with a knee injury during the 2-1 win over Fulham at the Emirates Stadium.
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There are also concerns over the fitness of Ben White and Riccardo Calafiori, who both missed the game against Fulham, leaving Arteta with a potential defensive injury crisis just days away from the crucial clash with Real at the Emirates Stadium on Tuesday.
On the injuries to his defenders, Arteta said: "Gabi felt something in his hamstring. We don't know how big that is and with Jurrien as well. He was already struggling very early in the game. He managed to continue, at some point he couldn't. So that's the downside to it.
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"The good thing is that it's been like this the whole season. How we have managed to be where we are with all those injuries, Ben White hasn't participated at all this season. It's what it is.
"You can imagine with those four players in the defensive line in one week. So Calafiori, Ben White, Jurrien and Gabriel. We have still another four that are so willing that they will do their job. We want it so much that we're going to give it a real go and we are very excited for the next week."
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Arsenal have already suffered hamstring injuries to Saka, Gabriel Martinelli and Kai Havertz this season.
Saka returned to the bench for Tuesday's league game but Arteta has been left to rue fresh defensive blows ahead of a crucial period.
'Gabriel's injury bad news for Arsenal'
Tim Sherwood reacted to Gabriel's injury on Soccer Special:
"Gabriel is holding his hamstring and needs to go down... this does not look good. This is really bad news for Arsenal as if it is bad, it could be his season over and they have Real Madrid coming up.
"He will not be the first player to do his hamstring trying to chase Traore!"
Analysis: Injuries sour Arsenal's winning night
Sky Sports' Nick Wright:
Saka's goal, scored with only his fifth touch, seven minutes after his introduction, provided a moment to savour for the home fans but Gabriel's withdrawal, and that of Timber later in the game, cast a shadow over their night.
Gabriel, whose partnership with William Saliba has become a major asset to Arsenal, looked despondent as he limped around the pitch and down the tunnel. His absence against Real Madrid would be a significant blow to Arsenal's Champions League chances.
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It appears just the latest in a series of hamstring injuries for Mikel Arteta's side. The Gunners will hope Gabriel's injury is not as severe as those of Saka, who missed three months, and Kai Havertz, who was ruled out for the season after breaking down in February.
Timber's enforced substitution, having suffered a knock to his knee in the first half, added another worry for Arteta, who rued the potential loss of four defenders in the space of a few days, with White and Calafiori also absent.
Arsenal's next four games
- Sat April 5: Everton (a), PL
- Tues April 8: Real Madrid (h), CL
- Sat April 12: Brentford (h), PL
- Wed April 16: Real Madrid (a), CL
How long could Gabriel be out?
Arsenal will be desperately hoping Gabriel's hamstring injury is not as severe as those suffered by Bukayo Saka and Kai Havertz earlier this season.
But even a grade one hamstring injury, a strain or pull where few muscle fibres are damaged, can take two to three weeks to heal.
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That length of absence could still rule Gabriel out of both legs of Arsenal's Champions League double-header against Real Madrid.
A grade two or three hamstring injury means a tear to the muscle and usually results in months rather than weeks on the sidelines, an eventuality which could rule Gabriel out for the rest of the season, like Havertz.
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Both Havertz and Saka required surgery, with Saka only returning to the squad for the first time on Tuesday night having suffered his injury in December.
Arsenal face Everton and Brentford in the Premier League either side of next week's first leg clash against Real Madrid on April 8. The second leg takes place on April 16.
Arteta: Saka lifted the stadium
The big positive of the night for Arsenal, however, was the return of Saka.
Saka scored on his injury comeback against Fulham at the Emirates, ending his 101-day absence when he came off the bench shortly after the hour mark.
The England international was on the pitch for just seven minutes when he doubled Arsenal's advantage before going to the dugout to embrace a member of the club's medical staff during the celebrations.
"I think a beautiful moment to see how much our people love, respect and admire Bukayo," Arteta said. "He's not a surprise to any of us and I think the best example is his reaction. Immediately after scoring a goal, what does he do?
"He goes and says thank you for all the hard work that all the sports science guys, physios and everybody involved in the recovery have done for him to be able to be in the condition that he is. I think he lifted the stadium, the energy and great to have him back."
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Saka, Martinelli offer positives amid Arsenal's injury woes
Sky Sports' Nick Wright at the Emirates Stadium:
Saka only needed seven minutes to mark his return to action with a goal. His close-range header from Gabriel Martinelli's flick proved decisive in Arsenal's 2-1 win over Fulham.
The 23-year-old, making his first appearance since December following his hamstring injury, had been given a rapturous reception when he emerged as a substitute but the celebrations which followed his goal were something else. "He lifted the energy in the stadium," said Arteta.
Saka looked sharp and so did Matinelli, whose acrobatic flick from Mikel Merino's cross to set up Saka's goal was one of five chances created in the game. Nobody else created more than two. Fulham struggled to contain him on Arsenal's left flank.
Like Saka, Martinelli has endured injury problems this season, but his return to form, coupled with the return of Saka, who now has a combined total of 23 goals and assists in 25 games for Arsenal this season, ensures an increase in firepower for the challenges ahead.