The victory puts Manly two wins clear of second-placed Penrith, who beat Canterbury across town, with five rounds to play and near certain to play at home in the opening week of the finals.
South Sydney can leapfrog Penrith with a win over Newcastle on Sunday but Manly, who have set the premiership pace for much of the season, could wrap up the minor premiership before the final round.
Before 12,873 fans, the Sea Eagles opened the scoring in the 12th minute when Lyon raced over outside poor defence from Dale Copley.
Manly had blown a number of sides away early at Brookvale Oval this year but a gritty Brisbane managed to hold their own in the opening stanza, even if both sides lacked polish in attack.
Jack Reed tied things up when he scored out wide in the 32nd minute after Daniel Vidot dished off a Ben Hunt kick.
But with a gusty wind against them, Manly should have gone into the break ahead after bombing three first-half tries.
Daly Cherry-Evans dropped the ball over the line just 66 seconds into the match after Brisbane began by putting the kick-off out on the full.
Lyon kneed the Steeden dead in the 23rd minute after he had won the race to a ball he could have easily picked up and Anthony Watmough dropped a Cherry-Evans pass three minutes before the break.
Broncos forward Matt Gillett was put on report for a 26th-minute hit on Steve Matai.
Back-rower Watmough left the game late with a knee injury, while Stewart missed the final minutes due to concussion.
Manly coach Geoff Toovey, who was Sea Eagles captain in 1997, praised the toughness of his troops.
"It was a great effort," he said.
"The fans didn't realise how much last week took out of us.
"We probably missed a couple of opportunities in that first 20 minutes.
"For 65 minutes, it could have gone either way."
Brisbane coach Anthony Griffin said his side still held their finals destiny in their own hands.
"I thought we did a pretty good job all night," he said.
"We just didn't take our chances. We made some bad decisions that released all the pressure.
"We have to win three games of football (to make the finals).
"We still have our chance to do that."
- AAP