The 20-year-old, who beat Federer en route to the Melbourne semi-finals in January, beat his French opponent 4-6 7-6 (7-4) 7-6 (7-4) to continue his fine form in 2019.
Should he complete his century in Saturday's final, Federer would become only the second man, after American Jimmy Connors, to reach 100 career tour titles.
After a brief interruption when the players were locked at 5-5 in the opening set, Federer saved two set points in the tiebreak and held firm to gain the upper hand in the contest. He will be looking for his first official win over Tsitsipas, after the Greek stunned him in the fourth round of the Australian Open where he was the two-time defending champion.
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"Reaching 100 titles - we're still far from it". The Frenchman, who came into the semifinals on an eight-match winning streak, broke in the third game of the second set when Tsitsipas double-faulted at breakpoint.
Federer has been stuck on 99 titles since October a year ago - a brief enough wait by any normal standards, but still a little frustrating for a man with his competitive instincts. "Beating the big guys, big players, players that have been in the top 10, means a lot to me".
Stefanos Tsitsipas booked a place in the Dubai Championships final after winning a thrilling encounter with Gael Monfils. "I was playing relaxed today, enjoying every moment". "I know that I'll have my work cut out against Borna".
"I'm going to have to.be patient, play with passion as well, wait for the opportunities to break him".
"I had some opportunities, I couldn't make them great today", said Monfils. I think I was up a break, and I didn't serve that good at the start of the second set.