Both sides traded chances in the opening 20 minutes, but it was Qatar that had the better of the looks with U.S. keeper Matt Turner twice stopping shots that looked headed for the back of the net.
Qatar was then handed a penalty after a video review when James Sands appeared to trip up Akram Afif in the penalty area, but Hasan Al Haydos skied his spot kick over the bar to keep the game goalless.
With the game looking like it was heading to extra time, Zardes popped up to poke home from close range after some nifty footwork from fellow substitute Nicholas Gioacchini to help his side to the showpiece final in Las Vegas.
Mexico has eight titles and Canada captured the top prize in 2000.
While the Qatar starting lineup on Thursday averaged 70 international games, the U.S. averaged 13 with an average age of 23 years, 284 days.
The match was played at Q2 Stadium, the home of Austin FC, which opened last month and will host the Americans' World Cup qualifier against Jamaica on Oct. 7.