Thomas, 23, has signed on for another two seasons with the A-League club while Makarounas, 21, has signed a one–year contract extension.
"It is a very pleasing outcome to have two young, talented players such as Lawrence and Jesse re-sign and commit to Melbourne Victory's future," Victory coach Kevin Muscat said.
"Both players have made valuable contributions to the team when they've been given their opportunities and they are both important players to our football club moving forward."
Thomas finished the season in goal after an injury to Nathan Coe, and played a key part in Victory's successful finals campaign.
With Coe since leaving the club, Thomas will battle it out with new signing Danny Vukovic to be Victory's first-choice keeper.
"Playing for Melbourne Victory is a great honour and to be continuing at the club for another two seasons is very exciting," Thomas said.
"Being a part of the success last season was an incredible feeling and the future at this club is very bright."
Makarounas meanwhile says he is 'looking forward to another successful campaign' after signing his deal.
"The opportunity to continue my career at Melbourne Victory was really important to me and I'm thrilled to be staying," he said.
