Phillips had been with Toronto since Day 1 in 2007. The native of Southampton, England, has been associated with the MLS since 1998, starting with Tampa Bay before moving to San Jose.
A club spokesman confirmed Tuesday that Phillips had left the club but declined further comment.
GM Tim Bezbatchenko started making changes in late August when he fired manager Ryan Nelsen and five assistant coaches. Greg Vanney, Nelsen's successor, was the ninth TFC head coach Phillips had worked with.
Philips' duties were all-encompassing. His years in the league meant there was little he didn't know when it came to looking after a soccer team, be it finding a place to do laundry on the road or finding a specific pair of boots on short notice.
Phillips returned to Southampton every December to see family and friends. A longtime Southampton supporter, he has a season ticket that a friend uses when he is on the other side of the Atlantic.
"I must be mad," he once said with a smile.
Not this season. The Saints are currently second in the English Premier League.