The 13.15.93 to 9.8.62 win, in front of a crowd of 33,606, was the Lions 13th in succession.
The victory will mean the Lions play Port Power in the qualifying final at the Gabba next week.
But the win wasn't assured until the second half with a well drilled Swans outfit and the heavy conditions combining to stop Brisbane's usual skilful running game.
The Lions had a nine-point lead at half time with their renown midfield lacking its usual strong influence on the game.
The exception was captain Michael Voss and on-baller Nigel Lappin.
The Lions were also well served through defenders Chris Johnson and Justin Leppitsch who continued to rebound throughout the match.
The Swans' Jason Ball was the best big man on the ground while onballer Daryn Cresswell and Jared Crouch managed to dampen the Lions game.
But the Lions in the second half proved they were as adept in the wet as they are in the dry kicking seven goals to four to win the match.
Lions goal-sneak Luke Power had a number of possessions and kicked two goals up forward while rover Shaun Hart increasingly made his presence felt.
For Sydney captain Paul Kelly and midfielder Stuart Maxfield battled hard during the second half.
Brisbane had named one of their strongest sides for the season with defender Darryl White coming back from suspension while ruckman Clark Keating and forward Alastair Lynch also returned.
But just prior to the game the Lions were forced to rejig their defence after in-form fullback Mal Michael was forced to withdraw because of the flu.
The Swans also had a late change with ruckman Greg Stafford pulling out.
Scoreboard:
BRISBANE LIONS: 4.3, 6.7, 9.13, 13.15 (93)
SYDNEY: 4.2, 5.4, 7.6, 9.8 (62)
Goals: Brisbane: L Power 2 T Notting 2 D Bradshaw 2 N Lappin 2 A Lynch J Akermanis J Brown S Hart M Voss. Sydney: T Kennelly 2 W Schwass D Lewis D McPherson P Kelly J Ball A Goodes G Bennett
Best: Brisbane: C Johnson M Voss S Hart N Lappin J Leppitsch D White. Sydney: D Cresswell J Crouch P Kelly J Ball S Maxfield.
Injuries: Brisbane: M Michael (flu) replaced in selected side by R Copeland. Sydney: G Stafford (groin) replaced in selected side by G Bennett, A Dunkley (back).
Reports: Nil.
Umpires: M Nash S Wenn A Coates
Official crowd: 33,606 at The Gabba
