Leipzig are an unpopular presence in Germany's top tier as their Red Bull backing is widely seen to have skirted around the league's 50+1 rule, where club members' must be influential in the boardroom.
But the side have been an overwhelming success on the pitch, finishing second in their first season in the Bundesliga last year to qualify for the Champions League.
While some were not happy to see Ralph Hasenhuttl's side perform so well, Rummenigge has been pleased to see their emergence.
"I praise Leipzig for several reasons," he told ARD. "First of all, they have worked well, you can see a clear upward trend.
"Leipzig are good for the Bundesliga. They quite simply deserve some respect. The Bundesliga should be happy."
Leipzig face Bayern for the second time in a week on Saturday – having been beaten in a penalty shoot-out by Jupp Heynckes' team in the DFB-Pokal in midweek.
Hasenhuttl's side sit third in the table after nine matches, one point behind joint leaders Bayern and Borussia Dortmund.