Guillaume Hoarau handed the hosts the lead in the 24th minute before Xhaka responded 15 minutes later with a brilliant effort from around 35 yards out.
The 27-year-old Albania international picked up a blocked shot and smashed his right-footed strike in off the crossbar.
An impossible effort to stop, certainly. The game would finish a point apiece as Marek Suchy doubled the visitors' advantage before Young Boys' Christian Fassnacht converted what proved to be the final goal in the 56th minute.
The result means Swiss Super League leaders Young Boys are ahead of second-placed Basel by 16 points.
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