Malaga native Banderas was a delighted spectator at the Rosaleda on Wednesday as the Qatar-owned Champions League debutants overturned a 1-0 deficit to 2004 winners Porto to advance to the quarter-finals 2-1 on aggregate.
Speaking to Spanish television broadcaster Canal Plus after the game, Banderas said he hoped Malaga's appeal against the ban at the Court of Arbitration for Sport would be granted.
UEFA said in its ruling published in December that Malaga had been sanctioned "due to the presence of significant overdue payables balances" and ordered the club to prove by the end of this month "that it has no overdue payables towards football clubs or towards employees and/or social/tax authorities".
"We are still waiting for the CAS decision and we sincerely hope that justice is done," Banderas said.
"It was an excessively harsh decision and has a negative effect on the Spanish league," he added.
"If this decision is ratified it will take away the motivation for a team that has to play against teams fighting to avoid relegation or to get into Europe.
"I think the decision is very misguided. It should have been taken at the end of the season giving the club time to settle these debts.
"I really hope CAS analyses the situation with a cool head and gives its backing to Malaga."
The Costa del Sol club have outperformed in Europe's elite club competition this season despite their institutional problems.
Wednesday's memorable 2-0 victory came after the club beat seven-times European champions AC Milan 1-0 in October on their way to topping Group C.
Banderas, who lives in the United States, said getting past Porto into the last eight was "an incredible triumph" for the club after years of ups and downs.
Malaga were paying in the second division as recently as 2008 and dropped to the fourth tier of Spanish soccer in the mid-1990s due to their economic woes.
Sheikh Abdullah Al Thani, a member of the Qatar royal family, bought the club in 2010 and some hefty investment helped them qualify for the Champions League with a fourth-placed finish last term.
It has not all been plain sailing, however, and the UEFA ban followed a turbulent few months when Al Thani's commitment to the project was questioned, wage payments were delayed and top players like Santi Cazorla sold to raise cash.
"I usually watch the matches on television from afar with nobody else around and suddenly I am here with my compatriots and it's really, really nice," Banderas said.
"Not just the football club deserves this but the city as well, deserves this joy," he added.
"It doesn't matter who we get in the next round because Malaga will enjoy themselves again.
"To be among the eight best teams in Europe this year for us is an incredible triumph for the fans.
"We have been suffering for many years. It's not only a fantastic thing for the team but for the city as well."