Sampras downplayed his victory, noting Federer was coming off a long season and that he was helped by his big serve and the fast indoor carpet surface. He had only aimed to win one set during the three-match series.
"Let's not get carried away," he said at a news conference.
Sampras ruled out a comeback from retirement, telling the audience after the match, "I had my time in the 90s."
Federer tried to put on a positive spin on the loss, saying he wasn't embarrassed to lose to his idol, but still showed some disappointment.
"It's been tough beating my idol the last two times. I'm happy that he got me at least once," he said, but adding, "I hope we can do it again in the future. I'd like to get him back."
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The two players have won a combined 26 Grand Slam titles, but Sampras, 36, retired five years ago after winning the U.S. Open in 2002. Twenty six-year-old Federer is fresh from another stellar season as he won three Slams and last week's Masters Cup in Shanghai in compiling a 68-9 winning record.
"I'm sort of surprised. This guy can play tennis, you know," the Swiss player said after his loss Saturday.
Federer beat Sampras 6-4, 6-3 in Seoul on Tuesday and edged the American 7-6 (6), 7-6 (5) in Kuala Lumpur on Thursday.