The game, held in Budapest's Puskas Arena, was the first major UEFA final to be held in front of spectators since the pandemic forced fixtures behind closed doors.
European football's governing body treated the event as a pilot to bring fans back to stadiums, with both teams being allocated 3,000 tickets with the remainder taken up by locals.
Those in attendance watched an intriguing encounter between last season's Champions League and Europa League winners, with the Bundesliga club coming out on top.
"We all know it is not easy to take the right decision," Bayern manager Hansi Flick told reporters when asked about the presence of fans.
"It felt good to have an atmosphere in the stadium. It felt a bit more like football. I hope all the fans return home healthy."
Bayern power on
Bayern needed extra-time to get the job done with Javi Martinez heading a 104th-minute winner in what could be his last game for the club.
Working tirelessly against the most in-form team in Europe, Sevilla had initially taken the lead after Lucas Ocampos' audacious 'no-look' penalty before Leon Goretzka leveled the scores in the second half.
The hard-fought win secured an impressive quadruple for Bayern in 2020, adding to the three trophies it won last season -- the Bundesliga, the German Cup and the Champions League.
Bayern is now unbeaten in 32 consecutive matches and has become the first team in Europe's top five leagues to win 23 consecutive matches in all competitions.
It won its last league match 8-0 against Schalke.
"It was an intense game but we deserved to win," Flick told reporters after the Super Cup victory.
"We are not yet fully in our rhythm despite our big win (8-0) over Schalke 04 on the weekend.
"But the mentality of the team, especially after going 1-0 down, was sensational. They battled back against very strong opponents and deserved the win."
The sight of fans watching live football will be a welcome return for many but there had been much criticism over the decision to allow thousands to attend.
Europe is currently facing a second wave of Covid-19 infections, stoking fears the game could cause a further rise in cases.
According to the World Health Organization, there have been 20,450 confirmed cases of Covid-19 in Hungary and 702 deaths, but like much of Europe, the country faces a second wave of cases with more than 6,000 infections recorded last week.
Those in attendance on Thursday had to abide by social distancing measures, such as remaining one-and-a-half meters apart, wearing face masks and undergoing a body temperature check on entry.
"The measures are strict and there is not a question of health risks for the fans," UEFA president Aleksander Ceferin said in a press conference before the game.
"We want -- and health is the number one priority -- to bring hope, to do what we think is the proper thing to do.
"Don't think we are doing this because of money because we don't get any revenue, we get more costs with it. But fans and players are [an] essential part of football."
However, photos from the match show not all fans adhered to the restrictions, with groups seen celebrating close together without face coverings.