Lewis, who has come in for some flak from supporters after recent blunders, kept out Luke Summerfield's spot-kick after Lee Frecklington had tripped Stephane Zubar in the third minute of injury time.
Posh had hit back after falling behind to Carl Fletcher's 38th-minute opener with second-half goals from Ryan Bennett and Craig Mackail-Smith, who struck his 30th of the season.
Posh manager Darren Ferguson hit back at Lewis' critics, saying: "Joe was absolutely outstanding for the whole game.
"The Plymouth goal is absolutely nothing to do with him. He has then made a stunning save just after we got in front before also keeping the penalty out.
"But I suppose in many peoples' eyes he will have been rubbish as usual, so there we go."
Source: PA
Source: PA