Rangers suffered more late heartbreak at Home Park, as a late Rory Fallon goal cancelled out Heidar Helguson's first half header.
The Icelandic striker - at the ground where he opened his Rangers account back in December- was the first to react to Adel Taarabt's deflected strike, nipping in between the Pilgrims back four and Roman Larrieu before burying an unstoppable header into the back of the net.
But all the R's hard work was undone in the fourth of five added minutes, when Fallon was incredibly fortunate to see the ball squirm off him and in for an unlikely leveller.
It was heartbreaking for the R's, who dominated for long spells in deepest Devon.
Magilton made five changes to the side that thrashed Exeter City in the Carling Cup just a few days earlier.
The R's gaffer recalled Peter Ramage, Gavin Mahon, Fitz Hall, Helguson and Taarabt to the starting XI, whilst goalkeeper Tom Heaton - who arrived on loan from Manchester United just hours before kick-off - took his place amongst the Rangers substitutes.
Most notably perhaps, Akos Buzsaky lined up against his former Club, in a wide left role.
Argyle were handed a pre-match boost with giant defender Krisztian Timar passing a fitness test, but new signing Cillian Sheridan had to make do with a place on the bench.
The assistant referees' were the busiest people in the opening exchanges.
Mr Flynn was on hand to flag Rory Fallon offside after his header found the back of the net, whilst Mr Bennett raised his flag to thwart Helguson as he bore down on goal following an audacious dummy from Taarabt.
It was Rangers who went closest in the opening exchanges, however, when Ramage's stooping header flew a yard over the bar in the tenth minute.
Moments later, Buzsaky - back at the Club whom he served so well before moving to Rangers - stung the palms of Larrieu with a 25-yard free-kick, as the R's began to force the initiative.
Midway through the half, Routledge - buoyed by his midweek treble - let fly with an audacious 35-yard half-volley, that had Larrieu pacing across his goal, as the ball flew a yard or so wide.
Another Buzsaky free-kick brought gasps of despair from the home faithful in the 25th minute, but this time the ball dipped inches over the crossbar.
Rangers were beginning to find their groove, with Routledge and Taarabt inevitably at the heart of their positive performance.
Indeed, it was the former who tested Larrieu on the half hour, as his 20-yard dipping effort was expertly tipped wide by the giant French stopper.
Taarabt and Buzsaky combined seconds later, playing a neat one-two that ended with the Moroccan international being denied by the sprawling Larrieu.
Rangers were really on top and their reward for a fine fist half display arrived two minutes before the break.
Taarabt's power and strength on the left flank proved too much for David McNamee and when his deflected effort bounced into the path of Helguson, the Icelandic front-man buried a textbook downward header beyond the outstretched dive of Larrieu.
It was no less than Magilton's men deserved, at the end of a half which they largely dominated from the first whistle to the last.
Sensing his side required more of an attacking threat, Paul Sturrock replaced Steve MacLean with Celtic loanee Sheridan at half-time.
The substitution resulted in a change in shape too for the hosts, with the Pilgrims switching to a 4-3-3 formation.
Magilton made a positional change of his own, with Taarabt and Buzsaky trading places, with the latter now being employed in the deep-lying front role he made his own during his Home Park days.
Taarabt's first act in his new wide role was to send a quite stunning curling effort into the side netting, when all and sundry in the Mayflower Stand thought the ball had nestled into the top corner.
It would have been a sensational strike from the Spurs loanee, but - to their credit - Argyle responded well.
Sheridan - who looked lively on his first appearance for Sturrock's side - sent a glancing header on target, but Buzsaky was in the right place, at the right time, to clear the ball off the line.
The same player was at it again on the hour, firing narrowly wide with a fierce left footed drive that arced away at the final moment.
Magilton made his first change soon after, with Patrick Agyemang replacing goalscorer Helguson.
The hosts had vocal appeals for a spot-kick waved away midway through the second period.
Fallon rose to meet McNamee's right foot cross, but when his backpost header was deflected wide, referee Mr East - who, to be fair to him, was perfectly positioned - declined the opportunity to point to the spot, despite raucous appeals from the Argyle players.
Buzsaky - who has been missing in recent weeks with a high complaint - made way for Hogan Ephraim with 17 minutes to play, as Magilton looked towards his diminutive attacker to make a difference.
Four minutes later it was the turn of Taarabt to take a breather, with Rowan Vine replacing the mercurial Moroccan, who himself had only returned from international duty 48 hours ago.
Vine's impact was instant, linking up efficiently with Ephraim, only to be denied a route on goal by a last-ditch Timar challenge.
The shaven-haired striker set up Routledge 10 minutes from time, but his sliced effort from the edge of the box flew well wide.
At the other end, it was the outstanding Hall who was on hand to pull off not one, but two expert tackles, as the hosts threatened to set up a Grandstand finish.
Play soon switched to the other end, and Vine was only denied by a full length save by the inspired Larrieu, as Rangers broke at pace from deep inside their own half.
But it was Plymouth who staged an unlikely late comeback in the fourth of five added minutes, as a long throw in to the box caused mayhem in the Rangers penalty area and the ball deflected off Fallon and into the back of the net.
Plymouth Argyle: Larrieu, Paterson (Duguid 86), Fletcher, Timar, Mackie, MacLean (Sheridan 46), Fallon, McNamee, Sawyer, Seip, Judge (Noone 82).
Subs: Arnason, Summerfield, Johnson, Letheren.
Scorers: Fallon (93)
Bookings: Fletcher
Red Cards:
QPR: Cerny, Ramage, Mahon, Hall, Leigertwood, Routledge, Helguson (Agyemang 60), Buzsaky (Ephraim 73), Gorkss, Borrowdale, Taarabt (Vine 77).
Subs: Stewart, Pellicori, Connolly, Heaton.
Scorers: Helguson (43)
Bookings:
Red Cards:
Referee: Mr R East
Attendance: 11, 558 (998 away)
