Clemens failed in his third attempt to earn his 300th career victory, watching the New York Yankees' bullpen give up the lead Saturday at Wrigley Field.
The Yankees wound up losing, 5-2.
Clemens declined to hold a post-game news conference, citing an upper-respiratory infection.
Clemens allowed just two hits in his first six innings against the Cubs. But after striking out Corey Patterson to start the seventh with a 1-0 lead, things fell apart.
Sammy Sosa - who hit his first career home run off Clemens - singled to left. Clemens then walked Moises Alou on five pitches.
Yankees manager Joe Torre called on his bullpen. As Cubs fans jeered and Clemens muttered, Torre patted the pitcher on the head and sent him back to the dugout.
Clemens had thrown just 84 pitches, 55 for strikes, in his bid to become the 21st pitcher to win 300.
Clemens had barely gotten a seat when Juan Acevedo gave up a long homer to Eric Karros on the first pitch, giving Chicago a 3-1 lead.
Karros had entered the game after a scary collision in the fourth inning sent Cubs first baseman Hee Seop Choi to the hospital.
Clemens got his 299th win on May 21 against the Boston Red Sox, his old team. But he failed in his next two starts, including last Sunday when the Yankees blew a 7-1 lead in Detroit.
Clemens' next start is likely to come Friday night at Yankee Stadium against St. Louis.
Choi was in serious condition after the collision, with pitcher Kerry Wood.
Choi lay motionless for a time after he was knocked to the ground and was taken off the field in an ambulance. He was admitted to Illinois Masonic Medical Center where Tim Curtis, the on-call administrator, said Choi was awake and talking.
With one out in the top of the fourth, Chicago put on a shift with New York star Jason Giambi at the plate. Giambi hit a high popup toward third, but third baseman Lenny Harris was near second base and had no chance at the ball.
Wood and Choi raced toward the pop, but neither had a great look at it in the sun. As they neared the third-base line, about 20 feet from home plate, they collided, with Wood's glove hitting Choi in the face.
Choi fell hard, slamming the back of his head on the dirt.
Four doctors and two trainers rushed to the field as Choi lay motionless on his back while his teammates huddled around.
Wrigley Field, which had been frenetic as Clemens tried for his 300th win, went quiet. Fans watched in silence as, first, a stretcher was called for, then the ambulance.
Wood, who was also knocked down, was able to get to his feet.
The game was delayed 17 minutes.
Choi, the first Korean-born position player in the major leagues, was replaced at first base by Karros.