The shot-stopper charged towards the South Bank at half-time of Wolves' loss to Bournemouth at the weekend and angrily pointed his finger and shouted at a supporter before stewards escorted a fan out of the stadium.
But O'Neil revealed in his pre-match press conference that Sa will play at Goodison Park.
"My main concern was how Jose was after it," O'Neil said of the incident.
"I've never done it but I'm guessing that would be quite a stressful and emotional moment for him. Firstly, to feel the need to go in to the crowd and then once you're in the crowd to check that he was OK.