The former Red Devils striker, who joined as one of Erik ten Hag's assistants in the summer, took caretaker charge after his Dutch compatriot was sacked in the wake of a 2-1 loss to West Ham United in late October.
Van Nistelrooy's four-match interim stint yielded three wins, against Leicester in the Premier League and League Cup and Paok in the Europa League, and a draw with Chelsea in the league.
The 48-year-old told the BBC of his stint: "I really enjoyed it, it's been a short but amazing period. We are in an uncertain position but we tried to do our jobs and help the club which is important."
"To close down this block of games with good results and a good connection I can't thank them enough. We will learn what the further plan is now."
Highly rated Sporting Lisbon coach Ruben Amorim will take over from Nov 11, with van Nistelrooy hoping to stay on as an assistant to the Portuguese.
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