The goal made Xhaka the third-ever Swiss player to score in multiple World Cups, joining Andre Abegglen (1934, 1938) and Jackie Fatton (1950, 1954) on the historic list.
Shaqiri also played in boots marked with the flags of Switzerland and Kosovo - the breakaway region that is not recognized as independent by Serbia or Russian Federation.
A dream start ensued for Serbia when Aleksandar Mitrovic headed home a cross from Dusan Tadic in the fifth minute.
With Mitrovic proving a handful for the Swiss defence, Serbia threatened to over-run their opponents and missed another chance when a corner flew across the face of goal and Dusko Tosic just failed to make contact. If the two teams end up with identical goal difference and goals scored, Switzerland would go through on the basis of head-to-head, thanks to Shaqiri's goal.
This is a tough one to call, but it is likely to decide who goes through to the last 16 along with Brazil.
Granit Xhaka had been "one of the few disappointments" in the 1-1 draw against Brazil, Swiss broadsheet Tagesanzeiger had felt. Serbian midfielder Luka Milivojevic had asked of the Swiss-Albanians. Serbia doesn't recognize Kosovo's independence and relations between the two countries remain tense. "But there is this history between them and the Albanians in our team, so it was not easy". At training Thursday, he wore football boots with Kosovo's flag on his right heel and the Swiss flag on his left. "They're trying to provoke us but we won't get dragged down to their level".
Both Xhaka and Shaqiri performed matching celebrations following their goals, interlocking their fingers in a gesture celebrating Albania.
Valon Behrami formed another luxurious axis in the heart of Switzerland's midfield, building on the sensational performance he put in against Brazil on Sunday, as he anchored the middle of the park judiciously, bringing composure and assurance to the midfield.
"I don't have any comments", Serbia coach Mladen Krstajic said. "You should always show respect", Switzerland coach Vladimir Petkovic said.
Switzerland, who came to Russian Federation ranked ahead of the likes of France and Spain, felt their way into the game as the first-half progressed. Mario Gavranovic, Josip Drmic and youngster Breel Embolo proved highly effective second-half substitutes who exposed a visibly tiring back line. The Serbia and Switzerland clash promise to be an all European cracker.