It was a sweet victory for Shaqiri and fellow Swiss goalscorer Granit Xhaka, who along with team-mate Valon Belrami were booed relentlessly by Serbia's fans throughout. Shaqiri is Albanian, born in Kosovo before moving to Switzerland with his parents and three siblings when he was just a year old.
"This is football, we did not convert some of our chances", Serbia coach Mladen Krstajic said.
Following the match, Xhaka posted a picture of his celebration on his Instagram story, with the caption in Albanian roughly translated to, "Here you go Serbia, this is why they call me Granit Kosovo!"
A 1-0 win over Costa Rica and Brazil's surprise 1-1 draw with Switzerland has left Serbia on the cusp of advancing from Group E in Russian Federation.
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The Kosovo War that ended in 1999 remains a contentious territory in both Serbia and Albania with the region now residing within Serbia, but having it's own Fifa-recognised team. His brother plays for Albania's national team.
After scoring the dramatic victor, Shaqiri wheeled away to the Serbian fans and crossed his hands over his chest to represent the Albanian Eagle. After causing Yann Sommer problems with his first header of the night, Aleksandar Mitrovic made no mistake with his second to put his side ahead with five minutes gone.
"You should never mix politics and football, it's good to be a fan and important to show respect", he told reporters after the game. The Swiss will advance to the round of 16 if they beat Costa Rica on Wednesday in Nizhny Novgorod.
Serbia had chances to score more before halftime. On the other hand, Switzerland's last game against Brazil ended up in drew and it will be the first time since the end of the former Yugoslavia an independent Serbia face Swiss side. Mitrovic came close in the 19th minute when he controlled a cross from Branislav Ivanovic on his chest and sent a bicycle kick over the bar.
Head coach Vladimir Petkovic could name the same side that drew 1-1 with Brazil, with Haris Seferovic continuing as a lone forward.
Shaqiri had been booed relentlessly by Serbia fans throughout a high-quality match, but the Stoke City forward had the last laugh with his last ditch victor.
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