The world number two won at the first extra hole at the Sheshan International Golf Club after the pair both finished on 19 under.
Schauffele, the defending champion, had birdied the 18th to take the event into a play-off but he could only score par as the pair played it again in sudden death.
McIlroy, who had to lay up after flirting with water on his first playing of the 18th, duly sank a birdie putt to claim his 27th career title.
It was also McIlroy's third win in a World Golf Championships event, his fourth win of 2019 and the first in his defence of the FedEX Cup title. It lifted him to the top of the PGA Tour's FedEx Cup standings and fifth in the European Tour's Race to Dubai rankings.
McIlroy told Sky Sports: "It's a tough closing stretch even though there are holes you think you should birdie. There are dangers waiting around every corner.
"I played conservatively when I needed to and thankfully it paid off."
McIlroy shot four birdies in his closing 68 while fast-finishing Schauffele recorded seven birdies, five of which were on the front nine, in a 66, although a bogey at the sixth was to prove costly.
South Africa's Louis Oosthuizen finished third on 17 under after a 69, two shots ahead of Victor Perez, Matthias Schwab and Abraham Ancer. Britain's Matt Fitzpatrick finished seventh on 14 under.
— PGA TOUR (@PGATOUR) November 3, 2019
McIlroy now hopes to round off 2019 with success on the European circuit's season-ending DP World Tour Championship in Dubai later this month.
The Northern Irishman said: "I got off to a good start in the FedEx Cup last year and being up there from the start is huge.
"I think this win gets me to number one in the FedEx Cup and that's nice going into the break. I'm going to take two months off after I play in Dubai in a couple of weeks' time.
"I am looking forward to that break but I have still got one tournament left this year at a place where I've had some success. I want to finish the year on a high note."