Mendoza's performance improved slightly in 2000 as he went 7–4 with a 4.25 ERA in innings pitched, including his first complete game since 1998, and last of his career. Despite his improved performance, he was left off of the postseason roster. The following year, he was 8–4 with a 3.75 ERA, and returned to the postseason. In the 2001 American League Division Series, he pitched in relief during three games and allowed only two hits with no runs allowed. In the Championship Series, he appeared in relief during three games and allowed one home run, (his only earned run in that series), pitching innings to a 1.69 ERA. In the 2001 World Series, he pitched innings of 1-hit ball as the Yankees fell to the Diamondbacks in seven games. In 2002, Mendoza pitched in 62 games to an identical 8–4 record with a slightly better ERA of 3.44. He pitched innings in the 2002 American League Division Series against the Angels, surrendering only two earned runs as the Yankees were defeated three games to one. On October 28, 2002 his contract with the Yankees expired and he became a free agent. An unnamed source from the Yankees said that they were concerned about his work habits and conditioning. He was on the disabled list each of the past three seasons. On December 30th, 2002, Mendoza signed a two-year contract with the Boston Red Sox.