The late victory lifted the Mariners to fifth place on the ladder.
Perth started furiously and had the Mariners pedalling back for the first part of the match.
French import William Gallas started a move in midfield and got on the end of a cross but hit the ball just over the bar with a spectacular overhead kick.
In their first attack the Mariners could have scored when Michael McGlinchey's firm shot was saved by Danny Vukovic and Matt Simon got first to the rebound but the striker lofted the ball over the bar.
Perth however took a deserved lead after 24 minutes when fullback Scott Jamieson found Jamie Maclaren with a deep pass and the striker cheekily lobbed the ball over the advancing Liam Reddy.
A few minutes after Gallas went off with a calf injury, the Mariners were on level terms just after the half-hour mark when McGlinchey got hold of a faulty clearance and slotted the ball home with a placed drive.
McGlinchey should have scored again on halftime when he hit the inside of Vukovic's post from a free kick that deserved better luck.
Ryan Edwards brought the best out of Reddy with a dipping shot as Glory threatened to take the initiative in the second half.
Mitchell Duke interrupted proceedings when he showed deft control before firing over tha bar with a sweetly struck volley.
Perth was forced to play the last 15 minutes with a man short after Jamieson was carried off with a leg injury and it had used all its substitutes.
The Mariners claimed the three points with a late, late goal from Duke.
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