Fernandez continued her giant-slaying run at Flushing Meadows, where the 19-year-old sensation has stunned defending champion Naomi Osaka, 2016 winner Angelique Kerber, No.5 seed Elina Svitolina and Sabalenka en route to the decider.
Fellow teenage sensation Emma Raducanu or No.17 seed Maria Sakkari await Fernandez in Sunday's (AEST) final in New York.
The defeat is a bitter blow for Belarusian star Sabalenka, who has never reached a major final, having also lost in the final four at Wimbledon this year.
The semi-final was full of momentum swings, but 52-23 unforced errors and 8-2 double faults ultimately were costly for Sabalenka, who lost the final game on her serve to love to hand Fernandez victory.
Sabalenka had raced to an early 3-0 lead inside 10 minutes on Arthur Ashe Stadium, dominating with her power, missing only one of her first 13 first serves, before Fernandez settled into the contest.
Trailing 4-2, Fernandez, the youngest woman to beat multiple top-five opponents at the same slam since Serena Williams in 1999, broke back as Sabalenka's first serve let her down, with the former converting the third of three break points.
Fernandez, who survived a break point to level it up at 4-4, eventually closed out the first set in a tie-break.
Sabalenka made a statement by breaking to love in the opening game of the second set, but Fernandez responded with a break of her own to level it at 2-2.
The second seemed destined for another tie-break, however Sabalenka broke to lead 5-4 and she never looked back as the 23-year-old forced a deciding set.
Fernandez seized control, breaking Sabalenka to move 4-2 ahead, though the latter responded immediately, despite the teenager taking her service game to deuce after trailing 0-40.
However, Fernandez held serve at 5-4 before breaking Sabalenka again to love to claim another memorable victory at the US Open.