Having seen off Uruguayan Franco Roncadelli in straight sets (6-4, 6-3) in the first qualifying round, Ymer took on 24th seed Cristian Garin of Chile, but after a slow start saw him lose the first set 6-2, the Swede battled hard in the second to force a tiebreak.
However, the unseeded Ymer was unable to force a deciding set and was beaten 7-5 in the tiebreak, thus 7-6 in the second set, marking the end of his championship, as Garin moved on to face Toby Samuel of Great Britain for a place in the main draw.
30-year-old Ymer was attempting to reach the first round at the US Open for just the second time, 11 years on from his only appearance. A second-round exit at the 2018 French Open remains his best Grand Slam performance, while this year's Australian Open is his only successful majors qualification for over two years.
His defeat ended Swedish involvement in singles play in New York, after Kajsa Rinaldo Persson was beaten in two sets (6-4, 6-3) by Serbia's Lola Radivojevic in the opening round of women's singles qualification. It was the 28-year-old Swede's first attempt to reach a Grand Slam tournament.
Swedish hopes now rest on Andre Goransson, who is expected to participate in the men's doubles with American Robert Galloway.