A young Bolton side lined up against a Palace team featuring the likes of Scott Dann, Steve Mandanda, Frazier Campbell and Zeki Fryers, however, it was the visiting Trotters who took all three points.
Despite the first-teamers in the Eagles side, it was the Wanderers who threatened first, Alex Samizadeh hitting the crossbar with his header.
This proved to be a warning sign from Lee’s side as minutes later Harry Brockbank gave Bolton the lead, firing home from just outside the box following Jeff King’s short free-kick.
The goal kicked Palace into gear and shortly following the opener, James Aspinall was tested twice in quick succession. Firstly, seeing Campbell’s effort drag wide of his far post before Phillips' header was calmly collected by the Bolton shot stopper.
Early in the second half, Jack Earing secured all three points with an incredible solo goal. Collecting the ball 40 yards from goal, the midfielder dribbled past a number of Palace players before finding the top corner of Mandanda’s goal from outside the box.
Speaking to bwfc.co.uk after the final whistle Lee said "Our team shape and discipline throughout the game was superb.
"We denied Crystal Palace any attacking chances and dominated the second period, playing attracting passive football and pressing really well.
"It was certainly a pleasing performance and playing at Selhurst Park against a Premier League Club was a fantastic experience for all involved.
"We are now second in the league and want to make it six wins in a row against Coventry next Monday."
Bolton: Aspinall, Spooner, Brockbank, Perry, Honeyball, Lavelle, Griffiths, King, Earing (White 90), Samizadeh (Politic 60), Newell (Fearnley 89).
Palace: Mandanda, Wan-Bissaka, O’Dwyer, Dann, Fryers, Phillips, Dreher, Lokilo, Flanagan, Kaikai, Campbell.