The former England international is due to appear in court later this month after allegedly being caught driving while three times over the legal limit last weekend.
Rooney returned to the Toffees' Finch Farm HQ on Tuesday afternoon for the first time since the arrest, having been given four days off by Koeman to rest.
According to the Daily Mail, the 31-year-old drove himself to training and linked up with the rest of his teammates, before then holding talks with Koeman.
It is claimed that Rooney has avoided any major punishment at this stage, as the Merseyside outfit will first await the outcome of his upcoming court hearing.
Koeman is scheduled to talk to the press on Thursday ahead of Everton's top-flight clash against Tottenham Hotspur.