The England forward suffered minor ligament damage in the Red Devils' Champions League quarter-final first leg defeat to Bayern Munich that was expected to sideline him for around two-three weeks.
However, the 24-year-old made a surprise return to the side the following week for the second leg against the German giants, but aggravated the injury early on in the encounter before eventually being substituted after 55 minutes.
Rooney, who missed United's goalless draw at Blackburn on Sunday, is believed to be in contention for the Manchester derby at Eastlands this weekend.
However, Van Basten - whose own career was cut short by persistent ankle trouble - says the striker must allow the injury to fully recover, otherwise he is jeopardising both his participation at this summer's World Cup finals and his career in general.
“When I saw Rooney limping against Bayern in the first few minutes I was begging for him to be substituted," he said in the Mirror. “I still cannot believe why Alex Ferguson, who I rate highly as a manager, did not take him off.
"I’ve been where Rooney was. I know what it is like. If your ankle is damaged and you get another heavy tackle on it the pain is always with you.
“It can do more damage, and a great striker needs to feel free of pain if you want him to perform. After hurting his ankle I could see quite clearly that he spent the rest of his time walking on his heels. That means pain.
“A top-class striker normally plays up on his toes, so he can sprint or go for every ball that falls in his direction.”
