Holding, who has been with the club since the age of eight, has been heavily linked with a move to the Premier League.
The highly-rated 20-year-old has reportedly attracted the attention of several Premier League clubs, including Arsenal, Everton and Bournemouth, and looks all but certain to move on in the summer.
According to The Bolton News, the club has already received a bid for the youngster, who was recently named their player of the season, with Arsenal reportedly his most likely destination.
The club's owners subsequently decided not to take the risk of an injury scuppering any potential deal, causing Holding to be left out their 26th defeat of the season.
Phillips told the local newspaper: “I was asked by the board of directors not to play him [Holding] yesterday. He was in the line-up on Friday morning but that’s as much as I know.
“It would appear some clubs are interested in him somewhere down the line. I think the wheels are still in motion on that one and it’ll be a few days before we get an outcome.”
The exact fee required to secure Holding's services remains unknown, but Phillips hopes the money raised from the sale will be reinvested into improving the team.
“If the deal goes ahead and the money is used to improve the squad as a whole then we can judge then whether it was a positive outcome," he added.
Saturday's loss at Craven Cottage means Bolton have finished the season without an away win for only the third time in their history.
Tom Cairney scored the winner 13 minutes from time, curling home after Ben Amos parried away a header from Matt Smith, condemning Wanderers to yet another miserable afternoon.