The South Korean winger was thrown on late in search of a goal which would have kept the Trotters in the top flight but sliced his chance off target
The 23-year-old winger was an 81st-minute substitute with the scores locked at 2-2 but couldn't help his team find a goal, which would have kept them up.
Earlier, Jonathon Walters had put Stoke ahead in controversial circumstances after clattering into Adam Bogdan who had two hands on the ball for the opener, but Bolton fought back with two goals before the break through Mark and Kevin Davies.
However, there was more controversy when Bogdan was adjudged to have brought down Peter Crouch for a 77th-minute penalty which Walters converted, before Lee's introduction.
And the South Korean had a chance when he met Marvin Sordell's cross, but he sliced his volley behind.
Ji Dong-Won (Sunderland): Was an unused substitute in the 1-0 home defeat to Manchester United.
Park Chu-Young (Arsenal): Didn't even make the squad for the final day 3-2 win at West Bromwich.
Park Ji-Sung (Manchester United): Was left on the bench as the Red Devils won 1-0 at Sunderland but it wasn't enough as Manchester City's last-gasp heroics earned them the title.
Jung Jo-Gook (Nancy): Wasn't in the squad for the 3-2 win over Saint-Etienne. Nancy sit 11th with one game to play.
Cha Du-Ri (Celtic): Was an unused substitute in the 5-0 victory over Hearts.
Ki Sung-Yueng (Celtic): Out injured for the win over Hearts.
Park Joo-Ho (FC Basel): Was an unused substitute in the 6-3 victory over Grasshoppers.
Kim In-Sung (CSKA Moscow): Not in the squad for the 3-1 final day loss to Rubin Kazan.
Lee Young-Pyo (Vancouver Whitecaps): Played a full game in the 4-1 defeat away to New England.
Lee Jung-Soo (Al Sadd): His side went down 4-3 on penalties to Al Gharafa, after a 0-0 draw in the final of the Emir of Qatar Cup.
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