New Zealand international Stott put her side ahead midway through the second half with her first goal of the season, adding to a first-half strike from Marianna Tabain.
Roar midfield star Katrina Gorry pulled a goal back to set up a nervy finale, before Stott added a second in injury-time with a classy finish.
Defeat for Brisbane ended the hopes of the two-time champions, who will miss out on the semi-finals for just the second time in nine seasons of the competition.
City will now face a winner-takes-all match-up against Newcastle Jets in the race for fourth in next weekend's final round.
Canberra United missed the opportunity to take top spot off Sydney FC as Western Sydney Wanderers claimed a shock 1-0 win at Campbelltown Stadium, leaving the race for the premiership wide open.
The Wanderers somehow turned around a record 10-2 defeat against bottom-side Adelaide last weekend to knock over the competition's in-form team.
A first-half strike from Katie Stengel proved to be the difference between the two sides in an end-to-end encounter.
Lively Wanderers' midfielder Erica Halloway hit the frame of the goal with a deflected effort, while at the other end teenage goalkeeper Jada Whyman was kept busy amid a flurry of half-chances for Canberra.
There was a blow for the Wanderers in the dying seconds with captain and Matildas defender Caitlin Cooper forced off with a knee injury.
American midfielder Arin Gilliland turned in a stunning virtuoso performance as Newcastle Jets upset leaders Sydney FC on Saturday evening.
Gilliland scored a second-half hat-trick in a 3-1 win against a side that had only conceded eight goals in 10 matches.