Shaqiri had joined up with the national set-up at the start of the week hoping to make his first appearance for his country since June 2019, but will now be quarantined.
He will miss Wednesday’s friendly with Croatia as well as the Nations League fixtures in Spain on Saturday and in Germany on October 13.
On Friday, Premier League champions Liverpool announced Senegal forward Mane had tested positive for Covid-19 four days after the club said new signing Thiago had the virus.
Mane and Thiago missed Sunday’s 7-2 humiliation at Aston Villa due to the virus while Shaqiri did not play either.