Australia had been pushed all the way by Malaysia in the contest before Adelaide product Brook broke the deadlock with a deft finish past Malaysian shot-stopper Firdaus Iman Mohd Fadhil to secure Australia's first AFF U-18 title in three years
The win was Australia's fifth overall AFF U-18 tournament win to draw them level with Thailand for the most titles in the competition's history.
It was an incredible bounce-back from the Gary Van Egmond-coached side, who were defeated 3-0 by Malaysia in the group stage.
The Young Socceroos controlled the tempo early on but lacked the cutting edge to break through a well-disciplined opposition.
Sydney FC rising star Marco Tilio was creating plenty of headaches for Malaysia's defence but still the Aussies were unable to find a breakthrough.
Malaysia, coached by former Socceroo Brad Maloney, had little opportunities to score in the opening 45 minutes, with their best chances coming from speculative long-range efforts which failed to test Australian custodian Kai Calderbank-Park.
Australia were lucky not to concede midway through the second half when Luqman Hakim spurned Malaysia's best chance of the game when he fired wide after a rapid counter-attacking move.
In the 75th minute Malaysia were forced into a goalkeeper change but substitute Irman Fadhil didn't have the best of starts with Brook sneaking in to score only moments after the replacement shot-stopper had come on.
There were a few nervy moments in the final minutes for van Egmond's side but they were able to cling on to hand Malaysia their second defeat after three consecutive finals appearances.