Bayern were without leading goalscorer Lewandowski as they suffered a 2-1 defeat to the defending champions at the Allianz Arena on Wednesday.
A shoulder injury sustained in the 4-1 Bundesliga victory over Borussia Dortmund consigned the Poland international - who has scored 38 goals in 42 appearances in all competitions this season - to the stands for the visit of Madrid.
However, Bayern chairman Rummenigge is sure their star striker will be ready to play in the return fixture at the Santiago Bernabeu next Tuesday.
"The medical department has done a great job, but the risk would have been too great [to play him in the first leg]," said Rummenigge, as quoted by Kicker.
"For the second leg he will 100 per cent be back."
Arutro Vidal's first-half header gave Bayern the lead, but the Chilean missed a penalty and a Cristiano Ronaldo double gave Madrid the win, his second coming after Javi Martinez was dismissed for two bookable offences.