The Austrians dominated the opening exchanges but failed to create many clear-cut efforts on goal, with their best chance falling to Marcel Sabitzer who hit the crossbar in the first half.
McClean, however, made no mistake just after the break when he slipped the ball through the legs of keeper Ramazan Ozcan to give Ireland all three points and a first victory over Austria since 1963.
"It's a massive three points for us," a delighted Ireland captain Seamus Coleman said. "He (McClean) has really taken to the green shirt in the last year. He's been brilliant since the Euros."
The hosts battered the Irish defence in the opening period, forcing three corners in the opening 10 minutes but there was little venom in the Austrian attempts on goal.
The Irish cause was not helped when midfielder Glenn Whelan had to be replaced by David Meyler in the 24th minute after suffering an injury, but the home side failed to take advantage.
David Alaba was unusually muted, the 24-year-old occasionally lighting up the game with a superb dribble, but often giving the ball away cheaply.
Austria's best chance came when Sabitzer saw his chip over keeper Darren Randolph bounce off the crossbar, with striker Marc Janko unable to stab home a squared pass from close range from the rebound.
That chance jolted the Irish into life and Jonathan Walters clipped the top of the crossbar as he lunged to reach Robbie Brady's whipped pass from the left.
McClean gave Ireland the lead early in the second half after Meyler launched a sweeping counter-attack before feeding the ball to Wes Hoolahan, who played it on for the winger to slot it calmly through keeper Ozcan's legs.
Austria poured forward in search of an equaliser and Janko had two excellent chances to equalise in the dying minutes.
However, both of his headers were off target, much to the delight of the 3,500 travelling Irish fans.
(Writing by Philip O'Connor, editing by Pritha Sarkar)
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