The opening exchanges saw few clear-cut chances. St Mirren keeper Ewan Anderson was first called into action after six minutes, tipping a cross from Brendan Hamilton behind for a corner. Bavidge had a shot comfortably saved before Blair Mckenzie put a header straight at Anderson.
After fifteen minutes the young Dons broke the deadlock. As they have so often, Liam Harvey and Bavidge linked up, Harvey flicking a long ball goal bound for Bavidge to run onto, and he rounded the keeper and made no mistake with the finish.
St Mirren responded with a chance of their own soon after, Elliot Dunlop looked a threat for the hosts, but Hamilton was able to clear off the line.
Minutes later Bavidge was at it again, latching onto a through ball from deep, blasting across goal and into the net.
Aberdeen saw more chances come their way in the remaining portion of the first half, but they were unable to extend their lead.
The second half couldn't have started in a worse way for Barry Robson's young side, Murray Campbell popped up at the back post to reduce the deficit and send Aberdeen a message that the game was far from over.
Daniel Devlin and Callum Penman kept the pressure on the Dons defence, with both players swinging inviting balls into the box, but there were no takers either time and Aberdeen retained the advantage.
The young Dons responded with chances of their own, Findlay Marshall played an inviting ball into the path of Alfie Stewart and McKenzie had another chance in the air, but Stewart's effort was saved and McKenzie was unlucky to see his cannon off the post.
The game became a scrappy contest as the heavens opened in Renfrewshire as St Mirren continued to push for an equaliser, but Blessing Oluyemi didn't have too much to do between the Dons sticks. Adam Emslie's play was stretching the Saints defence on the counter- his ball found Liam Harvey in the middle, but the effort went wide.
Soon after the centre forwards game was over and Cammy Wilson came on with just under ten minutes to play to try and see out the victory.
St Mirren made a claim for a penalty soon after the substitution when Hamilton went in hard on Dunlop, but the referee rightfully waved play on.
With six minutes left on the clock the skipper Dylan Lobban showed great energy, driving forward alongside Emslie who teed up Hamilton to swing an inch perfect cross into the box, where Bavidge was waiting to bury the chance, seal his hat-trick and secure the three points.
With St Mirren dead on their feet, Emslie ran through in the 90th minute and found himself one on one with the keeper, his shot was saved initially but he was first to react, snapping up the rebound and firing home.
In the end it was a comfortable 4-1 victory on the road for the Young Dons, but it was a gritty and battling performance that ensured the three points came back up North with them.