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Aleksandar Mitrovic handed Serbia the lead in the fifth minute during the match on Friday.
Switzerland equalised in the second half, thanks to a superb long range strike by Granit Xhaka (52nd).
Shaqiri (90th) found the winning goal in the final minute of regulation time .
Switzerland thus became the first team at this World Cup to clinch a come from behind victory after conceding first.
They now have four points from two matches, having held title contenders Brazil to a draw in their campaign opener.
They are at the same number of points as Brazil, but sit at the second place behind the South Americans due to an inferior goal difference.
Serbia are on three points from two games. They are currently third in the group.
Serbia enjoyed a promising start when Dusan Tadic won the ball near the corn er flag and sent in a cross which was headed in by Mitrovic.
The setback galvanised the Swiss who dominated possession for the rest of the game.
But despite being under considerable pressure, the Serbian defence prevented the Swiss from creating too many clear chances in the first half.
Switzerland finally made their domination count when Shaqiri's shot was bloc ked by the Serbian defence.
Xhaka pounced on the loose ball and unleashed a first time attempt from outs ide the penalty box which beat Serbia goalkeeper Vladimir Stojkovic with its pace and vicious swing before bulging the net.
Xhaka is the third Swiss player to score in more than one World Cup tournament.
He follows in the footsteps of former stars Jacques Fatton and Andre Abegglen.
Abegglen scored in the 1934 and 1938 World Cups while Fatton scored at the 1950 and 1954 editions.
Shaqiri hit the post soon after with a curling attempt from the right edge of the Serbia box.
Serbia did have their chances in the second half, not least a square pass across the face of goal by Aleksandar Kolarov which missed the extended leg of a Serbian player at the far post by mere inches.
Shaqiri found the winner in the closing stages off the counter.
He latched on to a pass out of defence, made a solo run from the half line with the Serbian defence caught off guard, before scoring with a calm finish.
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