France Football announced last week it would not select the world's best player this year due to a "lack of sufficient fair conditions" amid the coronavirus pandemic.
France's Ligue 1 was one of the leagues that were not completed, however, playing into the decision not to go ahead with the award.
Lewandowski has scored 51 goals in all competitions in the best season of his career, helping Bayern to win the Bundesliga and DFB-Pokal, while a treble bid remains very much alive in the Champions League.
Rummenigge thinks he would have been a worthy Ballon d'Or winner.
"I believe Robert Lewandowski is playing a fantastic season and he performed maybe the best season in his career," Rummenigge told a news conference on Monday.
"Unfortunately, France Football cancelled the Ballon d'Or, which we are not very happy [about]. In the end, it's not very fair - not just for Bayern but also for Robert Lewandowski, who might have won.
"I believe it's very important that in a season that, except the French league, [were] performed through to the end of the season, it has to be possible to give the Ballon d'Or to the best footballer in the world.
"Of course, I believe, in those circumstances, Robert would have a good chance to win it for the first time in his career."
Lewandowski has never been in the top three at the annual awards, but was fourth in 2015 after an excellent first season at Bayern.