The Dutchman returned to the club he represented as a player from 2001 to 2006 over the summer, joining Erik ten Hag's coaching staff as an assistant after the exit of former lieutenant Mitchell van der Gaag.
Van Nistelrooy subsequently stepped up to the role of interim head coach after Ten Hag was sacked, and a positive period at the helm saw him win three of his four matches in charge in all tournaments.
The 48-year-old masterminded a 5-2 EFL Cup beating and 3-0 Premier League success over Leicester City, as well as a 1-1 top-flight draw with Chelsea and 2-0 Europa League win over PAOK after temporarily replacing his former boss.
However, it was clear from the beginning that Van Nistelrooy was not a contender to take the job on a permanent basis, and Man United quickly wrapped up a deal for Ruben Amorim, who officially arrived at Carrington on Monday.
Man United confirm four coaching exits after Amorim arrival
Van Nistelrooy admitted that he was in the dark about his future under Amorim, who had been tipped to bring his own coaching team with him from Sporting Lisbon, and that appears to be the case.
On Monday evening, Man United announced that their club "legend" had departed at the end of his interim spell, while fellow coaches Rene Hake, Jelle ten Rouwelaar and Pieter Morel are also seeking pastures new.
"Manchester United can confirm that Ruud van Nistelrooy has left the club. Ruud rejoined in the summer and has taken charge of the team for the past four matches as interim head coach," Man United said in a statement.
"Ruud is, and always will be, a Manchester United legend. We are grateful for his contribution and the way in which he has approached his role throughout his time with the club. He will always be very welcome at Old Trafford.
"Rene Hake, Jelle ten Rouwelaar and Pieter Morel have also departed and we wish them all well for the future. We will confirm the full men's first team coaching composition in due course."
Where could Van Nistelrooy go next after Man United exit?
Details surrounding Van Nistelrooy's talks with Amorim will no doubt emerge in due course, but the latter has seemingly wasted no time in stamping his authority if the Dutchman is leaving straight away.
With an admittedly small sample size, Van Nistelrooy oversaw an immediate revival in Man United's fortunes during his short spell in charge, and it is not impossible to envisage him going straight into another Premier League job.
West Ham United's Julen Lopetegui and Southampton's Russell Martin are under severe pressure at the minute, and should either man be given the boot in the coming weeks, do not be surprised to see Van Nistelrooy linked with the positions.
Alternatively, the former Netherlands international could try his hand at Eredivisie management back in his homeland, while Italian giants Roma are also looking for a new manager after sacking Ivan Juric.
Elsewhere across Europe, Bundesliga strugglers Hoffenheim fired Pellegrino Matarazzo on Monday, and Van Nistelrooy has brief experience of the Bundesliga following his time with Hamburger SV in the 2010-11 season.