But the teams will meet again in Dortmund with the stands at Signal Iduna Park -- usually packed with 82,000 people -- empty after the Bundesliga became the first top European league to return, behind closed doors, following the coronavirus lockdown.
"It is a very special game," Flick said on Monday, with Bayern heading to Dortmund with a four-point lead.
"As a coach, there is no question that the fans are a missing factor."
Ten of the 18 league games since the restart have been won by the away team.
"The atmosphere can inspire any team. It is about how you can cope (without the support)," Flick added. "You have to accept the current situation and can't look for an excuse."
Bayern have restarted were they left off in March, following up a 2-0 win at Union Berlin with a 5-2 hammering of Eintracht Frankfurt on Saturday.
But Flick thinks Tuesday's clash will be a completely different test compared to their victory over Dortmund at the Allianz Arena last year.
"The conditions are very different compared to the first game," he said. "We've also had a good run and every player is a little bit more motivated."
Flick confirmed that midfielder Thiago Alcantara will miss out with injury, but Leon Goretzka will deputise again having impressed against Eintracht.
Jerome Boateng is fit to play after shaking off a knock and is set to partner David Alaba at centre-back.
That would mean no place in the starting line-up for Bayern's record signing Lucas Hernandez, who cost 80 million euros ($87 million) and is back after an ankle injury.
Standout matches today