Nicholas Hatzigeorgiou put a youthful Victory ahead early in the second half at Chaplin Reserve, but the host fought back.
Goals from Souheil Azagane and Dean Brotherston saw Sunshine secure a hard-fought win.
Victory head coach Gareth Naven said his team was punished for its mistakes in the second half.
"At 1-0, we looked all right. The second half was probably all about them," he said.
"We couldn't really get any control of the ball or we were in a position where we weren't confident of trying to get on the ball in certain situations.
"We were defending most of that second half and giving silly free-kicks away. If you haven't got an opportunity to tackle, don't tackle. Just stand up and wait until he makes a choice and then make a decision.
"But persistently giving free-kicks away creates pressure on us and that pressure does build up. Also, maybe made some more real poor choices in how to defend Sunshine's second goal I think.
"The players need to understand what danger is, where it is, the ability to see it and act on it and stop it. In saying that, we've got to think about how we execute things on the ball and it's a big focus for us, training the capacity to have a good touch, training the ability to pass the ball, especially when there's no pressure. If there's no pressure, we need to be able to secure the ball."
Neither side threatened in a scrappy first half, although Victory goalkeeper Stephen Hatzikourtis made a good save in an early one-on-one.
Just four minutes after the break, Hatzigeorgiou gave Victory the lead, the midfielder smartly turning inside in the area before finding the bottom corner.
George Cross responded through Azagane before Brotherston scored what proved to be a 67th-minute winner, cutting in from the right and finishing.
Earlier, Victory’s under-20s were edged 1-0 by George Cross.
Victory is away again in Round 24, making the trip to Bendigo City on Saturday, July 22.
PlayStation 4 NPL2 West 2017 Round 23
Sunshine George Cross 2 (Souheil Azagane 53', Dean Brotherston 67')
Melbourne Victory 1 (Nicholas Hatzigeorgiou 49')