The Premier League side were well supported at the Suncorp stadium and named a strong starting XI that included summer signings Danny Ings, Nathaniel Clyne, Milner and Joe Gomez.
Although they fell behind to a 17th-minute goal from Dimitri Petratos, they soon responded as Adam Lallana curled a shot into the far corner.
Brisbane provided better competition that Liverpool’s first tour opponents, Thai All-Stars, but Milner’s 75th-minute goal ensured the Reds came out on top.
Brendan Rodgers’ side might have thought themselves at home when the crowd of more than 50,000 gave a stirring pre-match rendition of ‘You’ll Never Walk Alone’ on a chilly evening more typical of Merseyside than tropical Queensland.
Brisbane, Australia’s champions for three of the last five years, matched the Reds in the early stages and opened the scoring when Petratos took two touches on the edge of the box before drilling the ball inside the post.
Milner and Ings both had chances to equalise before Lallana got the visitors back on level terms in the 27th minute.
It was Milner’s pass which found Lallana on the left side of the box and the midfielder beat his defender with a deft touch before curling the ball into the net with his right.
Liverpool pressed for a second goal before the break and went close when Mamadou Sakho had a header cleared off the line.
The Reds continued to control possession in the second half and Jordan Henderson was denied by a sharp save from the keeper.
Substitute Jordon Ibe also had an effort kept out before Milner struck the winner late in the game.
Taking the ball on the edge of the penalty area, he nutmegged one defender before his scuffed shot deceived the keeper and went into the middle of the goal.
Liverpool next face Adelaide United on Monday (10.30am BST) before heading to Malaysia and then Finland to complete their pre-season tour.