Christian Pulisic had become the first American man to score in an FA Cup final but his fifth-minute opener was canceled out by Aubameyang's penalty in the 28th minute after he was dragged down by Chelsea captain Cesar Azpilicueta.
A year into this pandemic-disrupted, longest-ever English season, Azpilicueta hobbled off injured in tears before halftime. Pulisic only lasted a minute after the break before also pulling up with an apparent hamstring injury.
With Chelsea unsettled by the injuries, Arsenal took control and Aubameyang chipped goalkeeper Willy Caballero from close range in the 67th.
It not only sealed Arsenal's fourth FA Cup in seven seasons but a place in the Europa League, having only finished eighth in the Premier League.
Chelsea's hopes of forcing the game into extra time were dealt a blow when Mateo Kovacic received a second yellow card in the 73rd after softly catching Granit Xhaka. Chelsea finished with nine men in stoppage time when Pedro was forced off with a shoulder injury.
Frank Lampard can still complete his first season as Chelsea manager by lifting a trophy but it would require the west London club first overturning a 3-0 deficit against Bayern Munich in the Champions League last-16 next Saturday.
But in only his 28th game in charge of Arsenal, Mikel Arteta won the FA Cup — just as he did as a player in 2014 and 2015.
“It was a lot of faith to bring me here and rebuild something special,” said Arteta, who replaced Unai Emery in December. “Hopefully we made the fans proud.”
The coronavirus pandemic restrictions meant this 90,000-capacity stadium featured no fans.
There could not even be a trophy presentation as usual in the Royal Box due to social distancing after this 139th FA Cup final. The players had to get their own medals before captain Aubameyang collected the cup on the pitch.
“I saw him walking with the bottom bit attached," Arsenal defender Rob Holding said, “and I was like, ‘You need to take that off!’”
A competition that began on Aug. 9, 2019, featuring teams from ninth and 10th tiers, ended later than it had ever done before — two months later than the final was scheduled.
Never before had the FA Cup final been staged without fans.
When the team buses arrived, just one man in an Arsenal supporter was singing by the entrance.
Inside the stadium, not even the traditional cup final anthem — “Abide With Me” — was sung live. Instead a pre-recorded version was played out, dedicated to the victims of COVID-19 and racial injustice and performed by Emeli Sande on the stadium roof.
“Love Justice Unity” appeared on the big screen on the stadium exterior that looks down Wembley Way where the only crowds were heading into the shopping mall.
Supporters were still heard inside Wembley before kickoff when an amalgamation of mental health conversations filled the silence at this final named after the Heads Up initiative spearheaded by Prince William, the FA president.
Not even the second-in-line to the British throne could secure a ticket to Wembley with the capacity limited to a few hundred, including players, club executives, media and medics.
It had been the dream start for Pulisic, who has been a revelation since the three-month shutdown of football ended in June.
Set up by Olivier Giroud’s back-heeled flick, Pulisic slotted in from close range after five minutes for his 11th goal in all competitions. The American emulated compatriot Carli Lloyd, who netted in the Women's FA Cup final in 2017 for Manchester City.
While Lloyd got to pick up the trophy after a 4-1 victory over Birmingham, this showpiece ended in agony for Pulisic.
Pulisic pulled up shouting in the penalty area at the start of the second half. He managed a shot before going down clutching his right knee. He had to be helped off the pitch, with support either side while he grimaced.