After delays and plenty of speculation, Football Federation Australia (FFA) announced its decision on Thursday.
The club from Melbourne will enter the competition in 2019-2020, while the Sydney side is set to join a season later.
"We have seen unprecedented interest from bids to be part of the Hyundai A-League and we are excited about our two new expansion clubs in Sydney and Melbourne," FFA chairman Chris Nikou said in a statement.
"An expanded Hyundai A-League will connect new communities in our two biggest markets, create new rivalries, bigger television audiences, more derbies and importantly, further opportunities for Australian footballers to play at the highest level in this country.
"One of the key factors in our decision was the long-term growth opportunity for each club in each new geography. South-West Sydney and Melbourne represent some of the biggest growth corridors in Australia."
They will be the first new outfits to join the A-League since the Western Sydney Wanderers in 2012-2013.
The bids beat four others, which were shortlisted in October, and all were from Melbourne, Sydney or Canberra.