Mariner lifted both the FA and UEFA Cups during an eight-year spell at Portman Road in the 1970s and 1980s and he was given a rapturous welcome when he entered the field before kick-off.
But he soon became the villain of the piece as a first-half header from Bradley Wright-Phillips and a late strike by substitute Joe Mason gave Argyle a win which breathes life into their campaign.
Plymouth are now just three points shy of safety and could climb out of the bottom three with victory at home to Blackpool at the weekend.
Town boss Roy Keane had seen his side climb to their highest league position of the season with three straight home wins but will be frustrated with a gutless display.
Wright-Phillips had the first effort on goal when he lashed a long-range shot wide before Daryl Murphy wasted a good chance to give the home side an early lead.
Carlos Edwards was involved in the build up and Murphy got on the end of his pass but scuffed his shot wide of the near post.
Murphy had scored six times in 11 starts since signing on loan from Sunderland and should have done better.
The lively Wright-Phillips was then denied by an athletic save by Brian Murphy before Ipswich centre-half Gareth McAuley headed a corner wide under pressure.
Mariner's visitors were posing a threat on the break and deservedly took the lead in the 34th minute.
The ball was worked out to Yannick Bolasie on the left flank and the winger easily skipped past full-back David Wright before whipping in a dangerous cross.
Wright-Phillips got ahead of his marker to easily steer a header past Brian Murphy and into the bottom corner.
Edwards hit a stinging shot from 25 yards as Town looked for an instant response but Argyle skipper Damien Johnson hurled himself across to make a brave block.
Town dominated the rest of the half but failed to test Plymouth goalkeeper David Stockdale.
The visitors made a bright start to the second period, with striker Jamie Mackie seeing one effort blocked by McAuley before curling a lovely effort past Brian Murphy from the edge of the area but a yard wide of the post.
Stockdale was finally called into action as he bravely beat McAuley to a header as the hosts struggled to raise the tempo.
Keane finally lost his patience on the hour mark, bringing on midfielders Owen Garvan and Grant Leadbitter in an attempt to win control.
Daryl Murphy then had their clearest sight of goal of the night but shot straight at Stockdale before Leadbitter saw a thumping 30-yard drive well saved by Stockdale.
Mason then came on for Wright-Phillips and joined him on the scoresheet with the second in the 78th minute.
Karl Duguid swept a pass across for Mackie and as defenders converged on the striker he slipped a pass square for Mason to tap in an easy finish.