Huntelaar was substituted in the 33rd minute after a collision with Madrid defender Raphael Varane and initial reports on social media claimed the Netherlands international had been diagnosed with a fractured fibula in his right leg after being taken to a local hospital.
However, Schalke announced after the first leg of the tie that the 31-year-old had watched the end of the match at the Veltins Arena, describing his injury as a "severe bruise".
"Huntelaar suffered a severe bruise. He was back at the Veltins Arena by the final whistle," the Bundesliga outfit wrote on their official Twitter account.
Roberto Di Matteo confirmed that Huntelaar had not broken his leg, although Schalke's coach was unsure when the prolific attacker might be available to play again.
"Nothing's broken [but it is] very painful. We can't say how long he'll be ruled out," the former Chelsea manager said at his post-match press conference.
Huntelaar is currently sidelined in the Bundesliga due to suspension after he was handed a four-match ban following his red card in the win over Hannover.
The Dutchman therefore missed the games against Bayern Munich, Borussia Monchengladbach and Eintracht Frankfurt and will serve the last match of his ban at the weekend versus Werder Bremen.