The penalty was levied after a mix up in the pits involving Richie Stanaway when the Kiwi came in for his mandatory stop at the end of Lap 10.
Stanaway's car was dropped back onto the floor with its left rear wheel not fastened, causing it to roll into the fast lane.
The rookie had started the race in 23rd position and ultimately finished one position worse off.
He was followed home by final finisher Will Davison, who made two pit stops during the 25-lap encounter, with Simona de Silvestro a DNF after incurring damage when she hit Jack Le Brocq early in the piece.
The penalty affects the pairing of Stanaway and Cameron Waters in the teams' championship, with teams of more than two cars split for championship purposes.
The Coates Hire Supercars Melbourne 400 continues tomorrow with Race 4 of the championship from 1240 local time/AEDT.