Scotland coach Craig Levein had warned not to expect a goal-fest against a team ranked 100 places below the hosts, but the Tartan Army only just managed to scrape the three points they desperately needed after claiming a point from their Group I opener in Lithuania on Friday.
Liechtenstein captain Mario Frick had more than just his 36th birthday to celebrate when he grabbed a shock opener - and his 15th international goal - for the visitors before Kenny Miller levelled for the shell-shocked Scots.
But it was McManus who had the final say with the decisive goal seven minutes into injury time to steer the campaign back on track and prevent serious questions being asked of Levein.
Levein opted for two up front with Kris Boyd making his first start in three years and partnering Miller.
James McFadden was also recalled after being named on the bench in Lithuania, while Lee Wallace was given the nod at left-back in place of the injured Steven Whittaker after proving his own fitness ahead of the match.
The Scotland boss had complained his players were not given enough protection from the referee in Kaunas and it took tonight's match official just nine minutes to produce a yellow card for Franz Burgmeier's crunching challenge on Alan Hutton.
McFadden presided over the resulting free-kick and supplied a lovely ball into the packed goalmouth, where Lee McCulloch rose above everyone else to connect with a firm header that he directed just over the crossbar.
Scotland had dominated the opening spell and were threatening again when Darren Fletcher - earning his 50th cap - slipped a quick free-kick to the feet of Boyd but he dragged well wide of target from distance, with an attempt on goal that was too ambitious.
The Middlesbrough forward had another chance when his former Rangers strike partner Miller did well to beat a couple of players before delivering to the back post where Boyd was waiting to nod home but Yves Oehri did enough to ensure the attempt was just off target.
With the match still deadlocked with the interval fast approaching, the visitors attempted to claim a shock opener when Sandro Weiser and Michele Polverino exchanged a one-two before Weiser's effort was smothered by Allan McGregor in the Scotland goal.
Liechtenstein's national anthem - the same tune as God Save the Queen - was jeered ahead of kick-off but the boos that rang around the stadium when the half-time whistle sounded were for very different reasons.
Levein used the break to make one change, with McFadden withdrawn and James Morrison introduced to the action. But, if the Tartan Army were unhappy at the end of the first half, they were stunned into silence at the start of the second.
Liechtenstein surged into the lead less than a minute after the restart when David Hassler whipped in a dangerous cross from the left for Frick and McManus stood off just enough to allow the skipper to rifle past the outstretched hands of McGregor.
There was more bad news for the Scots when Wallace was forced out of the action following a challenge from Martin Stocklasa, which earned him a caution, before Barry Robson was thrown into the action.
Robson's name was quickly added to the Ukrainian referee's book for his complaints after not being awarded a penalty after appearing to be caught in the face by goalkeeper Peter Jehle, who then prevented the home side drawing level when he punched a powerful shot from Fletcher to safety.
But he was picking the ball out of the back of the net with 63 minutes gone when Scotland hauled themselves level.
Morrison raced down the left flank before delivering into the box and Michael Stocklasa's headed clearance fell only as far as Miller who sent a superb left-foot volley high into the net.
Boyd made way for former Rangers club-mate Steven Naismith, who was involved in the action almost immediately when he went to ground under pressure from Martin Rechsteiner.
However, claims for a penalty were ignored when the referee deemed the challenge to be just outside the box and Robson's free-kick proved wasteful when his effort took a massive deflection and fell well off target.
McCulloch then capped what had been a disappointing night so far when he picked up a yellow card with just five minutes remaining to add to the caution he earned in Lithuania, which rules him out of next month's qualifier against Czech Republic in Prague.
Just when it appeared all hope was gone, McManus rose high in the box to meet Robson's corner and bullet a header into the back of the net deep into injury time as Hampden erupted in delight and relief.