The Pilgrims were not playing like a side deep in relegation trouble as they enjoyed some decent spells during the game, but Alan Judge spurned their best chance of a leveller when his penalty was saved by Brad Jones.
And Jonathan Franks' late strike made the result safe for the Teessiders.
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Plymouth, who are now four points away from safety, had a case for apenalty inside the opening 10 minutes when Jamie Mackie's strikeappeared to hit the elbow of a defender, but his appeals were wavedaway by the referee.
At the other end Middlesbrough, who seemed to be lacking ideas in attack, saw Barry Robson fire an effort over the crossbar.
Mackie again caused problems for the Boro defence when he set up achance for Bradley Wright-Phillips soon after, but the forward's effortwas deflected behind for a corner. From the resulting set-piece RedaJohnson sent his header wide of a post.
The Pilgrims wasted another chance to break the deadlock when Judge's corner was headed wide by Mackie.
And the hosts were made to pay as Middlesbrough took the leadagainst the run of play through on-loan Celtic defender McManus, whorose to head home Robson's free-kick after 22 minutes.
Plymouth tried to find an instant response with Johnsonorchestrating a good move upfield but, when the ball eventually fell toWright-Phillips, the former Southampton man shot straight at Jones inthe Boro goal.
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Paul Mariner's men were gifted the perfect chance to level matterswhen Justin Hoyte was adjudged to have handled Judge's effort threeminutes before the break.
Judge tried to place his penalty into the bottom corner of the netbut Jones did excellently to palm the ball away to his left andpreserve the visitors' slender advantage.
Middlesbrough came close to doubling their advantage within threeminutes of the restart as Lee Miller headed the ball over DavidStockdale, but Leroy Lita could not make enough of the opportunity.
Lita, who was booked for an alleged dive in the first half, enragedthe home supporters when he again appeared to go down unchallenged butfortunately for Boro he escaped a potential dismissal.
Boro were enjoying the better of the chances in the second half as Robson's left-footed drive was parried by Stockdale.
Plymouth were not going to go down without a fight and Johnsonheaded over the bar shortly after the hour mark as the hosts searchedfor an equaliser.
Mariner's men almost got their reward in stoppage time, but Johnson's header was excellently tipped over the bar by Jones.
And that miss proved costly as Franks netted from long range deepinto added time, meaning Boro have now not lost in seven league visitsto Plymouth.
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