The result means the two clubs are level on four points in Group C, five points behind leaders Paris St Germain, who crushed Anderlecht 5-0.
Olympiakos opened the scoring in a rain-hit Lisbon through attacking midfielder Alejandro Dominguez in the 29th minute.
But it was the former Benfica keeper Roberto who was key to the final outcome.
Roberto, returning to the Luz stadium as Olympiakos' No. 1, failed to clear a corner in the 83rd minute and Cardozo pounced to earn his side a precious point.
"We could have played better. Now we have to win in Greece and hope that Paris St Germain beats (Olympiakos) too," Benfica striker Lima told Portuguese radio. "The fight for second spot is between us and Olympiakos."
Olympiakos coach Michel told UEFA.com: "We were better today than Benfica. I am proud for my players. They displayed their personality and tough mentality.
"We did not hide and looked Benfica in the eyes. We prevailed throughout the match, with or without water on the pitch."
Olympiakos' Kostas Mitroglou, who scored a hat-trick in the previous round, was a constant headache for the Lisbon club's defence in the first half.
He fired just wide when through on goal from a tight angle and then floated a header near the post.
It was Mitroglou who provided the assist for Dominguez with a clever back heel, and the Argentine then confused centre back Ezequiel Garay with a dummy before slotting home.
The rain was so heavy the ball often got bogged down in midfield, forcing both teams to opt for a direct style of play.
And the surface water denied Olympiakos a second goal when a shot from David Fuster found a puddle instead of rolling in.
"We wanted to win but in the Champions League every point is important. Our players fought a lot, including against this rain," said Benfica coach Jorge Jesus.
"The match demanded of a lot physical and mental strength because of it, and we lived up to it."
In the end, 27-year-old Roberto, who made a flying save from a Cardozo free kick in the opening minutes, lost focus for a second and the Paraguayan did not spare him a second time.