Tries to Dale Copley and Connor Watson opened up a 14-0 lead after 28 minutes.
But the Broncos all but erased that margin by halftime when a double strike by Anthony Milford and James Roberts ensured the score was just 14-12 at the break.
Roberts' try would have particularly upset Roosters coach Trent Robinson with winger Daniel Tupou spilling a second-tackle kick by the Broncos to gift the home team a try.
Brisbane were lucky to still be in the contest after a half in which they completed just eight of 15 sets and made 23 tackles inside their 20 to none by the Roosters.
Scores were levelled 11 minutes into the second half and then a sweeping move put Jordan Kahu over in the 56th minute for the Broncos to hit the front for the first time.
The Broncos dominated the remaining minutes but it took a broken-play break by Roberts in the 75th minute and then a quick-thinking grubber to find Kahu which ensured the Broncos took out the match.
Ex-Bronco Copley, whose first-half try was his third this year against his old club, failed to complete the opening stanza when he was knocked out trying to tackle Kahu.
It's Copley's third concussion this season and comes just three weeks after being knocked out in the seventh minute of the Roosters' shock round-23 win over the Cowboys.
The Roosters' 18th loss of the season ensures the Tricolours - minor premiers the previous three seasons - will end the year in 15th.
