Estevao doubled his side's lead just before halftime but was showing signs of fatigue before the break. In the second half he fell to the ground and vomited before being carried off around the hour mark.
He remained unwell on the bench and was given medication by the Palmeiras medical staff during the match, which was played at an elevation of around 3,650 metres.
"It took me a while to get used to it and unfortunately I couldn't continue," he told Paramount+. "It was really a matter of the altitude. It's surreal here."
Estevao's replacement Mauricio went on to score the winner as Palmeiras made it three wins from three in Group G.
Chelsea signed Estevao last year for a reported fee of 29 million pounds ($38.54 million) and he is set to join the London side later in 2025.