The Rebels looked to have scored in the 75th minute of Sunday's game at AAMI Park, which would have levelled the match with a conversion from in front, however the TMO ruled a double movement by prop Cabous Eloff.
With the Brumbies down a man with lock Darcy Swain yellow-carded for cynical play, Melbourne continued to hammer the line but couldn't break through the Brumbies' defence.
The result pushed the Brumbies back up into second spot on the ladder while the Rebels remain outside the finals-bound eight.
Snubbed for Jones's first Wallabies camp, with Gordon called in for the first time, Lolesio made a statement in the first half before the Brumbies halves were replaced after 55 minutes.
The 12-Test playmaker scored two tries, showing some rare emotion after both.
With Jones watching from the stands, he thumped his chest after the first and after the second yelled "Carter Gordon" after touching the ball down.
He told commentator, former Wallabies winger Drew Mitchell, it was "personal".
"It's a bit personal this game but I will keep it on the field," Gordon said as he walked from the field at halftime.
Despite Lolesio crossing twice it was a fairly even battle between the playmakers, with Gordon showing his toughness in defence while he set up two tries by firing cut-out passed to winger Lachie Anderson.
Gordon also bagged one of his own in the 71st minute when he swooped after a loose Brumbies pass to touch down.
The game was level at 14-14 after 22 minutes, with Brumbies fullback and Test hopeful Tom Wright showing his pace to cut through the defence for Lolesio's first five-pointer.
Melbourne's first try was scored after a barn-storming run by flanker Josh Kemeny in the second minute.
Tries to flanker Jahrome Brown through the Brumbies powerful maul either side of half-time pushed their lead out to 28-14.
Melbourne skipper Brad Wilkin limped from the field before his team closed the gap with Anderson diving across for his second.
However the Brumbies' physicality bore fruit through their Test flanker Rob Valentini, who barrelled over the line after 12 phases.
The 62nd minute try proved enough to keep the Rebels at bay.
