Robben sustained a torn calf muscle 16 minutes into his comeback from a five-week injury absence and Lewandowski broke his jaw and nose and suffered a concussion after a clash with the Dortmund keeper on Tuesday, Bayern said.
The Poland international, however, sounded hopeful he could still be ruled fit to play in their Champions League semi-final first leg at Barcelona next week.
“It’s a few more days til the match at Camp Nou, I really hope I will be able to play,” he wrote on Twitter.
The latest injuries are especially bitter with Robben and Lewandowski involved in 45 percent of Bayern’s 117 goals in all competitions this season.
There is nothing positive in a defeat,” club CEO Karl-Heinz Rummenigge told reporters. “We just have to shake it off and take the pitch next Wednesday in Barcelona with renewed vigour.”
“Maybe we have some better luck there,” he said, with Bayern already missing Franck Ribery, David Alaba and Holger Badstuber.
Dutchman Robben has had a stellar season, scoring 17 league goals until his injury in March.
Lewandowski, who was knocked down in a rough challenge by Dortmund goalkeeper Mitch Langerak, broke his upper jaw and nose and suffered concussion.
The in-form Poland striker had scored nine goals in his last 11 matches for the Bavarians, who secured the Bundesliga title last week with four games to spare.
Bayern said more medical checks would be required to determine the length of Lewandowski’s absence.
There was some good news amidst the gloom with Thiago, who returned recently after a year out injured, having suffered no major damage from a knock on his thigh.
Bayern’s 2-0 defeat on penalties to Dortmund, with all four Bayern players failing to score from the spot, meant they missed the chance to repeat their 2013 treble.
(Reporting by Karolos Grohmann, editing by Justin Palmer)