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The Portuguese winger, making his first start since returning from an ACL injury, played in the 1-0 win over Kilmarnock.
It was Jota's first start in a year-and-a-half, but O'Neill had always intended to assess his fitness at half-time.
The Celtic manager said: "Jota, that was his first start. I didn't expect him to last.
"I maybe thought he might get 60 minutes in the game, but he was really tiring in the last 10 minutes before half-time.
"I said to him before the game, 'I don't expect you to go the whole way, I want to see how it is at half-time.'"
O'Neill noted that Jota's fatigue was particularly noticeable when "chasing back."
Yang, who replaced Jota, was praised by O'Neill as being "ready to go" and "brilliant for us this season."
The decision to sub Jota was not due to any injury concerns.