Victoria 169 and 8 for 285 (Short 119, Johnson 5-72) lead South Australia 114 (O'Neill 4-28) by 340 runs
A low-scoring contest was turned on its head as Short mastered the tricky Junction Oval pitch to score 119 - a tally nearly three times better than any other batter in the match.
The century continues a rich vein of form for Short, who broke through for his first 50-over century last week, more than seven years after his senior debut.
Victoria ended the day at 8 for 285 for a massive 340-run lead that seemed highly improbable just 24 hours earlier.
South Australia's lower order capitulated earlier in the day. Having resumed at 5 for 75, they were dismissed for 114 to concede a 55-run first-innings deficit.
Short played a major role in building that advantage, with his 70 off 69 balls on day one more than double the next best for either side in the first innings.
In the second innings, he punched 15 boundaries and a six in his 135-ball knock of 119, and it took some fancy footwork to dismiss him, with Jordan Buckingham taking a juggling catch on the boundary rope.
At the time of his dismissal, Short had, incredibly, scored some 36 percent of the runs in the match across the three innings.
Maxwell made just 5 in the first innings, though his dismissal came via a contentious lbw decision.
Earlier, in his first game back after suffering a broken leg, Maxwell left the field during SA's innings after being struck on a wrist by a ball when fielding at slip.