Poland's Swiatek fell on her back and covered her face with her hands after prevailing in a tight second set tiebreak, having sealed the win when the fifth seed's shot sailed long.
It was twice French Open champion Swiatek's first major title on a hard court and the 21-year-old is the first Polish woman to win the U.S. Open.
Despite the defeat, Jabeur will regain her world number two ranking when the tournament concludes on Sunday.
Jabeur made history at Wimbledon when she became the first Arab woman to reach a major final. She added another line in the history books in New York, becoming the first African woman to reach the U.S. Open championship match.
Swiatek came out firing, pushing Jabeur to the back of the court with her precise serve and deep groundstrokes to race to a 3-0 lead.
Jabeur found the range with her forehand to win back-to-back games for 3-2 but the momentum was short-lived as Swiatek broke back and took the 30-minute first set when the Tunisian's backhand landed in the net.
A confident front-runner, Swiatek kept the pressure on early in the second as frustration began to mount for Jabeur.
Swiatek blasted a backhand winner down the line for a 3-0 second set lead and it seemed the match would be a brief affair.
But urged on by a rowdy and supportive crowd at Arthur Ashe Stadium, Jabeur rallied to force a tiebreak.
However, she made some costly unforced errors that opened the door for Swiatek, who exchanged a warm embrace with the Tunisian after improving to a 3-2 lifetime record against her.