Legspinner Mitchell Swepson trapped Jon Holland lbw for a duck with seven balls left late on Friday to secure the 60-run win.
Holland and fellow tailender Chris Tremain (18 not out) had hung on grimly for nearly nine overs.
It is Victoria's third loss from four games, while Queensland are second on the ladder with two wins.
Victorian opener Eamonn Vines appeared hard done-by when he tried to evade a short ball down the leg side, but umpire John Ward gave him out for the second wicket.
The replay strongly suggested the ball had only brushed his shirt on the way through.
Then Queensland were adamant they had won the game when Tremain was caught at second slip off the bowling of debutant Blake Edwards with seven overs left.
Tremain did not budge and this time Ward ruled it had come off the pad.
Victoria, who have won four of the last five Shields, were well-placed after tea on day three when Queensland lost the seventh wicket in their second innings and only led by 89 runs.
But a stubborn 88-run partnership from captain Jimmy Peirson and fellow tailender Mark Steketee proved the counter punch that turned the game.
It took a sharp catch from Victorian captain Peter Handscomb at wide first slip off James Pattinson's bowling to remove Steketee on Friday morning for a top score of 52.
Peirson was unbeaten on 51 as Queensland were dismissed for 306 before lunch, setting up a run chase of 190 for Victoria.
After reaching 41 without loss, Victoria bled wickets amid rain delays and tight Queensland bowling.
Handscomb, who top-scored with 92 in the first innings, only made three when he attempted a pull shot off debutant Blake Edwards and chopped onto his stumps.
That left Victoria teetering at 3-52 and needing a massive partnership from Aaron Finch and teenage newcomer Jake Fraser-McGurk.
But Fraser-McGurk (19) and Finch (17) fell in quick succession and the home side were on the ropes at 5-85.
After his hat-trick in the first innings, Swepson snared 3-17 as opener Matt Short top-scored with 27.
Pattinson was a rare highlight for Victoria on Friday, taking two wickets to finish with 4-66 in the Queensland second innings.
The paceman was recalled to the Test squad on Thursday and he continues to put his shocking injury run behind him.
Pattinson shouldered a 48-over workload this week and took six wickets.
Fellow Test paceman Peter Siddle, who also dug in with Tremain for the eighth wicket, took 3-58 in the Queensland second innings.