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 now have four points from two matches.
Serbia have three points from two games.
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
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