Fourth seed Rublev broke Tsitsipas twice in the opening set and put the second-seeded Greek away with a dominant tie-break to secure victory in 97 minutes.
Stefanos Tsitsipas will next play another Russian in fourth seed Andrey Rublev who battled past French qualifier Jeremy Chardy 7-6 (7/2), 6-7 (2/7), 6-4.
Erste Bank Open: Novak Djokovic saves four set points to beat Borna Coric, virtually assured to end season World No. 1
Novak Djokovic will play either Hubert Hurkacz or Lorenzo Sonego in Friday's quarterfinal.
Djokovic has been the top-ranked player at the end of a season five times. Should he beat Borna Coric, he will equal the achievement of his childhood idol, Pete Sampras.
The 33-year-old Serb has been the top-ranked player at the end of a season five times: in 2011, 2012, 2014, 2015 and 2018.
Saint Petersburg Open 2020: Andrey Rublev, Borna Coric set up final clash with wins over Canadian opposition
Third-seeded Rublev rallied to beat second-seeded Denis Shapovalov 4-6, 6-3, 6-4, and Coric also recovered in the semi-finals to beat Milos Raonic 1-6, 6-1, 6-4.
Zverev edges past Harris to reach Cologne Open semi-finals; Rublev advances to last four at St Petersburg open
Hard-serving American Reilly Opelka, who beat defending champion Daniil Medvedev at St Petersburg Open on Thursday, was beaten by the seventh-seeded Borna Coric 7-6 (3), 6-3 in their quarterfinal.
Italian Open 2020: Fuming Paire shows little effort in opening-round loss; Nishikori earns first win for year
Kei Nishikori — who is returning from right elbow surgery and missed the US Open after testing positive for COVID-19 — won for the first time in more than a year, beating Albert Ramos-Vinolas 6-4, 7-6 (3).
US Open 2020: Carreno Busta downs Shapovalov in five sets to reach semi-finals; Osaka races past Rogers
Alexander Zverev also reached the last 4 of the US Open as he bounced back from a shocking start to oust 27th-seeded Croatian Borna Coric in four sets.
The 23-year-old Zverev said he stepped on the gas after finding himself a set down, and 4-2 behind in the second set.
US Open 2020, Quarter-finals, Tennis Highlights: Pablo Carreno Busta to face Alexander Zverev in last-four; Naomi Osaka vs Jennifer Brady in semis
Follow all the latest action, live scores and more from the US Open 2020 quarter-finals on Firstpost.com's live blog!
US Open 2020: Borna Coric stages epic comeback to stun Stefanos Tsitsipas; Novak Djokovic sails into last 16
Croatia's 27th seed Borna Coric staged a remarkable Houdini act to stun fourth seed Stefanos Tsitsipas in a 4hr 36min late-night thriller.
Novak Djokovic, Coric, Grigor Dimitrov and Viktor Troicki all tested positive during the Adria Tour event in Serbia and Croatia, which was later cancelled.
Novak Djokovic's Adria Tour event lacked bit of common sense, says former ATP players' council head Vijay Amritraj
Djokovic has apologised and admitted it was probably “too soon” to run the event, which was played in front of packed stands in Belgrade.
'I feel well and don’t have symptoms': Tennis star Borna Coric says after contracting COVID-19 infection
Coric was among several other players who tested positive for COVID-19 after playing in Novak Djokovic’s controversial Adria Tour tournament.
'Protocols are in place for reason', Wimbledon chief expresses disappointment over botched Adria Tour
Wimbledon chief said, 'The images were disappointing and I think that ... what needs to come out of it is everybody involved — not just players, but administrators, organisers, entourages — understands that the protocols, rules and regulations are in place for a reason.'
Novak Djokovic goes from aiding lower ranked players to endangering countless in miserably quick fall as role model
Djokovic is not being berated for failing to live up to the lofty expectations that come with the territory of being an all-time great; he is being slammed because he behaved like a stupid, selfish jerk.
Djokovic tested positive on Tuesday after taking part in a tennis exhibition series he organised in Serbia and Croatia, becoming the fourth player to test positive for COVID-19.
After Grigor Dimitrov, Borna Coric, Viktor Troicki test positive for COVID-19 having played in Adria Tour exhibition event
Borna Coric and Viktor Troicki tested positive for COVID-19 after playing in Novak Djokovic’s Adria Tour exhibition event, raising serious concerns for tennis governing bodies in their bid to restart the sport after a lengthy shutdown.
Coronavirus Outbreak: High-profile cases at Novak Djokovic's Adria Tour tennis event put sports under scrutiny
With high-profile coronavirus cases of Grigor Dimitrov and Borna Coric emerging from Novak Djokovic's Adria Tour tennis event, sports tournaments in Serbia and Croatia have come under scrutiny