But the former England striker had to be treated with bandages and take painkillers in the first half after suffering what looked like a nasty hand injury when he was stood on by an opponent.
Tests, though, have confirmed no serious damage has been caused, so Rooney is in contention for Sunday's home match against Burnley, with the status of defensive duo Michael Keane (foot) and Phil Jagielka (hamstring) less certain.
"Wayne had a scan on his hand this morning and it is fine - there is no fracture," Koeman said at his pre-match media conference.
"I hope to have some positive news on Saturday - we need to make a decision about Michael Keane and Phil Jagielka whether they are available for Sunday, but they are doubtful.
"It's always important to have everybody available, because all these players are quality, experienced players and that's what you need in a difficult situation."
On midfielder James McCarthy's recovery from a knee injury, Koeman added: "He needs game time first in the Under-23s to play - that's how players need to come back after a long time being injured."
Everton are looking to lift spirits after the Apollon draw, which left them bottom of Group E and followed a difficult start to the Premier League campaign that has left Koeman under pressure.
"I'm too long in this job to lose my confidence, but yes, I'm worried about the situation and how we can turn it around," said the Everton boss.
"I have enough confidence to be the same manager as I was for the past six or seven years, when I was successful.
"Football can be strange, football can be difficult, but Thursday can't be compared to Sunday because the opponent is totally different.
1 - Everton are the first English side to pick up just one point after their first two Europa League group stage games. Glum. pic.twitter.com/gEXEi5LLRC— OptaJoe (@OptaJoe) September 28, 2017
"If we win maybe we are back, but if we don't win Monday will be totally different and that is football.
"Maybe [the players' fear came from] the pressure to win the game. We try to analyse everything, but we are human people.
"The situation [in the league] was possible to expect when we knew all the fixtures in the beginning.
"You can see it as really negative for our position in the Premier League, but you can lose against Chelsea, Tottenham and Man United. We played 10 more games and we lost one of 10. It's not all so negative."