A few supporters left at half-time but the majority stayed to the end as their team played their last Champions League game at Camp Nou until at least 2024, with the team set to move to the city's Olympic Stadium next season during renovations.
Barca fans had already mourned their impending, and now confirmed, exit over the past fortnight and despite defeat, the match didn't become the funeral procession it might threatened to.
"Thanks to the fans for their unconditional support, there was an extraordinary atmosphere, we have to thank them and show them the respect they deserve," Xavi told Movistar.
"It's a pity that we weren't able to show them that on the pitch. We have to disconnect from the Champions League, face the reality.
"We did not compete today, we did not reach their level. They were very good, much better, more intense. I am sure the elimination before the game affected us psychologically."
A cut above
Bayern, already through, were without injured goalkeeper Manuel Neuer, defender Lucas Hernandez and winger Leroy Sane, but still put out a strong line-up and clinically took the lead after 10 minutes.
Serge Gnabry played a fine through ball for Sadio Mane to race on to, leaving Hector Bellerin chasing hopelessly behind, and the Senegalese forward lofted over Marc-Andre ter Stegen.
Bayern sliced Barcelona open like a hot knife through butter again in the 31st minute, with former Stoke City and PSG striker Choupo-Moting finishing consummately after another Gnabry pass. The Cameroon international now has five goals in his last four games.
Julian Nagelsmann's team could have added a third before half-time but the otherwise ragged Hector Bellerin blocked on the line and ter Stegen denied Jamal Musiala from close range.
Moments later Barcelona won a penalty when Robert Lewandowski was felled by Matthijs de Ligt, but after watching the incident again, referee Anthony Taylor cancelled it, provoking vitriol from Camp Nou.
Gnabry had a goal ruled out for offside in the second half just when it seemed Bayern had again masterfully absorbed Barcelona's pressure and sucker-punched them at the other end.
Bayern rounded off their victory in stoppage time when Pavard finished from close range after a corner was fired back his way.
"We wanted to give the fans a win but it couldn't be, we owe them a lot, they have always been with us," Pedri told Movistar.
"We owe them wins and titles, I hope that going forward from now, we can give them that. We have to improve a lot, we have to be self-critical and keep moving forward because there are a lot of trophies to fight for.
"We'll do everything we can to win the Europa League, as last year we couldn't do it."
Former Bayern striker Lewandowski, who swapped the Allianz Arena for Camp Nou in the summer, left frustrated again, unable to net against his old side, one of the favourites for Champions League glory.
Barcelona will be among the favourites in Europe too, albeit for a different trophy.