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Rooney, who rejoined Everton from Manchester United in July, ended his 14-year England career when the country's all-time leading scorer announced his international retirement on Wednesday.
Everton hold a 2-0 lead over Hajduk Split from the first-leg of their Europa League qualifier and travel to Croatia for the second leg on Thursday. Progression to the group stages, means the Merseyside club will compete in four different competitions.
"He had a talk with the national coach and made his decision, because he thinks it is the best for Everton," Koeman told reporters. "It is always the player's decision and, of course, I respect that.
"If you reach the group stage of the Europa League and have international duty, then that is a really tough programme.
"His fitness is really good at the moment... I think it is a good decision for him and a good decision for Everton. It means when the internationals come, he will have some time at home with his family."
Koeman, who earned 78 caps for the Netherlands as a player, also said that he did not advise Rooney, who scored 53 goals for England, on his decision to retire.
Following their Europa League tie, Everton travel to Premier League champions Chelsea on Sunday.
