Lendl, who has slipped to 18th in the world rankings, reached the semi-finals with an emphatic 6-3, 1-6, 7-6 win over the second-seeded Becker.
The defeat meant none of the top three seeds made it into the last four. Edberg, the No 1, was beaten 6-4, 6-4 by the American, Todd Martin, while the third seed, Chang, lost 4-6, 6-3, 7-6 to the unseeded Greg Rusedski, of Canada.
Lendl, who has won the Tokyo title four times, had been through a dismal season until arriving in Japan, losing in the first round of nine tournaments and winning only one event. But the ninth seed was back on form yesterday and consistently passed a frustrated Becker, who saw his first serve desert him in the tie- break.
Lendl last beat the German in the fourth round of the 1992 US Open and yesterday's win put their career head-to-head score at 11-10 in the Czech-born American's favour.
Michael Stich, the world No 4, underwent tests in hospital in Bolzano, Italy yesterday, after falling ill after eating breakfast. He later returned to his hotel, but he withdrew from the doubles event. He had lost in the first round of the singles earlier in the week.