In a hectic finish Phillips put Birmingham back in the game after Bolton had led from the tenth minute with a Tamir Cohen goal.
Bolton, however, stormed back and, after Matt Taylor had hit the post from a free-kick, Lee followed up to produce the winning goal and their second successive away win.
The game marked the end of an era for Birmingham's power-brokers, Karren Brady, David Sullivan, and the Gold brothers, David and Ralph, following the take-over of the club by the Hong Kong Grandtop group.
But Bolton did not read the script and the game was hardly the kind of result to mark the end of their 16-year association.
Birmingham's new-look side, keen to improve their league position, were in a positive mood but it was Bolton who created the first shock of the game when they steamed ahead after only ten minutes.
A seemingly harmless throw-in by Sam Ricketts was headed on by Kevin Davies and Cohen's looping header went into the far corner of the net for his third Premiership goal of the season.
Surprisingly Birmingham failed to lift the pace as Bolton appeared in control with former Aston Villa defenders, Gary Cahill, Zat Knight and JLloyd Samuel in commanding form.
England boss, Fabio Capello, must have been impressed with the ever-improving form of Cahill who certainly lived up to the tag as the best young central defender in the Premiership.
Birmingham's ploy of operating with a lone striker was hardly a success as Christian Benitez was shut out completely by Cahill and Knight and, in the second half, the home fans gave vent to their feelings as they chanted 4-4-2 hoping to persuade manager Alex McLeish to change his tactics.
As it was, their best chance of an equaliser in the frustrating first half came in the 31st minute when Teemu Tainio shot wide from Gregory Vignal's left-wing cross.
A minute later Jussi Jaaskelainen had to be on his best form to make a reflex save to keep out a Cahill deflection and this set up some concentrated attacking play from Birmingham.
Vignal hit the crossbar but the equaliser continued to elude Birmingham in their desperate bid to consolidate a middle of the table position.
Fabrice Muamba, another player being watched by Capello, produced a solid performance thwarting his former Birmingham colleagues with some good work in midfield.
Eventually McLeish conceded to the Birmingham fans' demand to send on Garry O'Connor as a replacement for Tainio seconds after substitute Lee should have increased Bolton's lead on the hour.
The final 30 minutes were a tale of Birmingham attacking in depth and Bolton defending their slender lead with great determination.
Phillips scored a fine equaliser when he took a return pass from Benitez to score with a low drive in the 83rd minute only for Lee to destroy their hopes of a point with a winner two minutes later.