The Young Matildas dominated the early stages and took the lead after 12 minutes through a Cortnee Vine goal.
Vine doubled the lead just before half-time, finishing from a Princess Ibini-Isei cross.
Australia missed a penalty in the 62nd minute, but it turned out not to be costly as they put the result well beyond doubt with two goals in as many minutes during the closing stages of the match.
The victory at Myanmar's Mandalarthiri Stadium, with three points and a clean sheet, was the ideal start to the tournament for coach Craig Deans and his squad.
It puts them in a commanding position to progress from Group B, which, in addition to Malaysia, contains host country Myanmar and Timor Leste.
The tournament features two groups, and the top two teams from each will progress to the semi-finals, with the winners to meet in the final on 4 August.
It is worth noting that the AFF Women's Championship is a senior, open age competition - but all 23 players in the Young Matildas squad are 19 years old or under.
Australia U20 Women next face Timor Leste, before their final group game against hosts and two-time tournament winners Myanmar.
