"It hurts to have to say so but I don't think we can make it," said the World Cup-winning captain and coach. "Congratulations to Werder for the German title."
Second-placed Bayern dropped nine points behind Werder with 14 games remaining after losing 1-0 at VfL Bochum on Saturday.
"If we were six points back I would say we could still make it because we still have a home game against Werder but nine points is too much," Beckenbauer wrote in a column in Tuesday's Bild daily.
Werder closed in on a fourth German title that would be their first since 1993 by beating Kaiserslautern 1-0 on Sunday courtesy of a penalty in added time.
"Realistically we now have to fight for second place," wrote Beckenbauer. "We can live without a title. What's important now for us is to qualify directly for the Champions League."
Bayern have dropped out of the German Cup but remain in contention in the Champions League. They face a daunting task against Real Madrid in the first knockout round.
