Van Aert, winner of three stages in the race and leading both the mountain and points classification, was forced to pull out on Tuesday after a heavy fall in the 16th stage.
His team reported: "Wout Van Aert did not suffer a fracture in his fall on the Vuelta.
"The 29-year-old rider did however pick up a serious knee injury requiring intensive medical care."
The team added in the post on social media that Van Aert was returning to Belgium to continue his recovery.
Van Aert has endured a tough 2024, suffering multiple fractures after a bone-crunching high speed fall in March in the Tour of Flanders which forced him to miss the remaining Spring one-day classics.
But he returned in good form and picked up an Olympic time-trial bronze medal in Paris in July.
Tuesday's latest tumble has thrown into doubt his participation in the road world championships in Zurich at the end of the month.
