Saints striker Jonah Ayunga ensured his new side weren't the victims of a cup upset after producing a clinical first half brace at Central Park.
The summer signing bagged his first goal for the club early on against Cowdenbeath, turning cleverly past two defenders before firing into the bottom corner to break the deadlock.
And he doubled St Mirren's lead shortly after when he tapped home from Joe Shaughnessy's flick on from a corner.
While the Buddies struggled to break down their stubborn opponents in the second half, they still returned to Paisley with a welcome first competitive win of the season tucked neatly under their belts.
Stephen Robinson handed a first competitive start to young goalkeeper Peter Urminsky, who started between the sticks in place of the injured Trevor Carson.
Summer signing Ryan Strain made his competitive debut for the Buddies, slotting in at right back with fan favourite Ryan Flynn reinstated in the heart of midfield.
St Mirren started the game on top, pressing the Lowland League side and earning three early corners which all came to nothing.
Centre back Charles Dunne split the defence with an excellent pass after breaking up a rare Cowdenbeath foray forward. He picked out Alex Greive on the left wing, who couldn't quite pick out a teammate in the box with the danger eventually cleared.
Saints keeper Urminsky was a spectator in the early stages of the first half but the 23-year-old had to be alert to deny Scott Sinclair's powerful free-kick.
The striker's low effort was goal-bound before Urminsky's smart stop at the bottom right hand corner.
Just before the 20 minute mark the visitors made their dominance count. Young forward Kieran Offord did superbly to keep the ball in play before setting up Ayunga in the box.
The striker's clever turn beat two defenders before he powered home his first competitive goal for the club with a fierce low strike that nestled in the bottom corner.
The dust had hardly settled before the summer recruit grabbed his brace. A floated corner kick was knocked on by Joe Shaughnessy to the back post, with Ayunga gratefully tapping home his second from close range.
The first half petered out in the Fife sunshine, with Cowdenbeath resolute at the back and St Mirren already starting to take their foot off the gas.
Flynn flashed a cross into the box after a clever turn on the left wing just before the break, with Cowdenbeath's defence just scrambling the ball clear to stay in touching distance of the Buddies.
The visitors returned from the break unchanged, looking to press home their advantage and give the travelling support something more to shout about than just their beautiful new black away kit.
It was Cowdenbeath who threatened first in the second period though, with Charles Dunne coming to the rescue to block substitute Chris Aikamhenze's shot after he burst past Shaughnessy into the box.
Robinson took the opportunity to mix things up on the hour mark.
Greg Kiltie, Toyosi Olusanya and Richard Tait replaced Flynn, Offord and Scott Tanser as the Buddies looked to spark some life into a forgettable second half.
Saints had another let off when Shaughnessy's attempted clearance from a cross failed to connect.
Thankfully for the skipper the Cowdenbeath striker wasn't positioned well enough to make him pay for his mistake.
The Saints almost made it three when a good old fashioned stramash in the box saw the ball pop to striker Greive's feet.
The New Zealand international's snapshot clipped the top of the bar with keeper Mason McCready well beaten.
St Mirren made further changes in the closing stages, with youngsters Jay Henderson and Celtic target Dylan Reid both introduced late on.
Tait tried his luck from distance with a fizzing strike that had a concerned McCready at full stretch, but the ball sailed narrowly wide of the post.
In truth it was a forgettable second half performance from both sides, only brightened up when Cowdenbeath almost nabbed one back with a long range effort that had Urminsky scrambling.
Thankfully for him it dropped just over the bar, allowing the imposing keeper to walk away with a clean sheet from his first start for the club.
