The three had been charged by Federation Internationale de Football Association over the incidents which took place during Switzerland's World Cup Group E match against Serbia in Kaliningrad on Friday, where they celebrated the goals by making the sign of the eagle in reference to the Albanian flag.
The Swiss overturned a 1-0 deficit to provide the 2018 World Cup with its first comeback win of the tournament, with Xhaka's thunderbolt from outside of the box tying things up, and a late counter seeing Shaqiri seal it the win at the death following Aleksandar Mitrovic's opener.
Xhaka and Shaqiri are both ethnic Albanians from Kosovo, which broke away from Serbia in war in 1999 and declared independence nearly a decade later but is not recognised by Serbia.
Lichtsteiner has been fined CHF 5,000 with the trio all warned over their "unsporting behaviour contrary to the principles of fair-play".
"In football you have always emotions and you can see what I did and it's just emotion", Shaqiri told reporters, referring to his controversial celebration after the match.
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The world football governing body does not allow the imagery of political messages or symbols in stadiums.
"My family had left Kosovo before the war broke out, when I was four years old, and they tried to make a life in Switzerland with me and my two brothers", Shaqiri wrote on the Players' Tribune website ahead of Friday's match. I'm very happy to score this goal. Serbia does not recognize that independence. "It's not more. I think we don't have to speak about this now".
"We are not clear how the German referee could have been appointed for the match between Switzerland and Serbia, when it is well known that one of Swiss confederation cantons is a German canton", Serbia said in its statement.
Xhaka and Shaqiri are of Kosovar heritage and their celebrations greatly angered Serbia's FA, with their president condemning and claiming a "brutal robbery" had denied the Balkan side of a win last week . The gestures were meant to mimic a two-headed eagle, which is an Albanian national symbol.
Swiss coach Vladimir Petkovic after the match reproached the players, saying that soccer and politics should "never mix".