Philipp Lahm and Xabi Alonso both slipped and Mario Gotze’s penalty was saved before Manuel Neuer sent his spot-kick against the crossbar.
Pep Guardiola was full of praise for his side’s performance, though.
He said on the club website: "I’m proud of my team as never before. You can’t criticise your team when they’ve played so well. I’m very proud of my players. We did everything we could and I’m happy with that.
Dortmund boss Jurgen Klopp added: "That was the game from hell. We were lucky, no question about it."
Lewandowski said he hoped he would be fit for the away clash with Barca in a week’s time.
"Its a few more days till the match at Camp Nou, i really hope i will be able to play!" he said on Twitter.