Suzy Shepherd's side needed to win their final fixture at New Tinto Park if they were to seal top-flight football next season, but were beaten by the hosts who join SWPL 2 champions Dundee United as the teams to go up.
After a goalless first half, Glasgow Girls grabbed the lead from the penalty spot ten minutes after the restart, Kaitlyn Canavan on target from 12 yards. On-loan Hibernian Women's Lucy Ronald made it two nine minutes later before Thistle gave themselves a lifeline through a Novoa Torrente finish. But any hopes were dashed when Mhairi Lyle added a third 12 minutes from time.
Boroughmuir finish the season in third spot and can be enormously proud of their efforts this year.
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Meanwhile, in SWPL 1, Hibernian Women and Glasgow City played out a goalless draw at the home of Penicuik Athletic.
The hosts carried more of a threat but were unable to find the breakthrough. Dean Gibson's side finish fourth in SWPL 1.
Elsewhere, Hearts finished their campaign on a high after a 3-0 victory over Partick Thistle at Oriam.
The Jambos, who secured eighth spot, were ahead inside 90 seconds through Holly Aitchison's header. Aimee Anderson added a second 12 minutes into the second half and Maria McAneny rounded off a fine afternoon with a third late on.
Sixth-placed Spartans were also victorious, Kat Smart and Alana Marshall on target in the first half in a 2-1 win over Hamilton Accies at the Fountain of Youth stadium.