Serbia's players did not react to the eagle gestures at Kaliningrad Stadium.
Shaqiri scored a late game-winner and Swiss fans lost their minds. A draw will be enough for Mladen Krstajic's side only if Switzerland lose vs. Costa Rica by two goals. Switzerland have participated in the last three World Cups and European Championship - 27 points in the qualification is remarkable!
One team that has definitely taken notice is Serbia.
9 - the number of World Cup matches Nati captain Stefan Lichtsteiner has now played for Switzerland, breaking the national record held by Charles Antenen since Chile 1962. Serbia 1-0 Switzerland. Mitrovic's goal remains the difference between the two sides going into the halftime.
Switzerland wasted little time in finding their equaliser after the break with Granit Xhaka pouncing on a blocked Shaqiri shot and firing an unstoppable blast from outside the box past a helpless Stojkovic on 52 minutes.
"If there are such Albanian patriots, why don't they play for that country?"
After scoring the dramatic victor, Shaqiri wheeled away to the Serbian fans and crossed his hands over his chest to represent the Albanian Eagle. "They're trying to provoke us, but we won't get dragged down to their level".
And Serbia head coach Mladen Krstajic is braced for a hard encounter, telling Swiss newspaper Blick: "They are very strong!"
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.
Both made the double Albanian eagle with their hands when scoring, in a celebration full of symbolism and dedicated to their loved ones.
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.
All eyes will be on Juventus, Manchester United and Real Madrid target Sergej Milinkovic-Savic again after his dazzling display but it could be Aleksandar Mitrovic's time to shine. Mario Gavranovic, Josip Drmic and youngster Breel Embolo proved highly effective second-half substitutes who exposed a visibly tiring back line.
Xhaka was playing a lot more freedom with a change of system, his through ball on the edge of Serbia's penalty area found Steven Zubar but former Chelsea full-back Branislav Ivanovic knocked it away from his toes just in time. Switzerland's greater energy, combined with Serbia's inability to keep their shape in the latter stages, won the day.