Croatia captain Domagoj Vida found out at half-time of his country's 3-3 draw with Turkey that had tested positive for Covid-19.
The 31-year-old defender, who was already scheduled to be withdrawn after 45 minutes, was immediately isolated from the rest of the squad.
Vida and the rest of his Croatia team-mates had tested negative on Monday but the Besiktas centre-back's Wednesday morning test came back positive as the first half ended.
A Croatia statement read: "The medical service of the Croatian national team received initial information at the end of the break between the two halves that there was one potentially positive result. This is a common test procedure, and a 'suspicious' finding is retested to confirm the result.
"As at that time the coach Zlatko Dalic had already made the decision to change (Domagoj) Vida, the medical service of the national team isolated Vida according to all epidemiological measures until the confirmation of the test results.
"Vida will, in accordance with regulations, spend the next few days in self-isolation in Istanbul.
"All other national team members and staff members, who tested negative, are scheduled to travel to Stockholm. It is taken into account that the national team complied with all epidemiological measures, in accordance with UEFA's Return to Play protocol."
Vidal will self-isolate for 10 days while the rest of the squad prepare to be tested again before their UEFA Nations League fixture with Sweden on Saturday.
Croatia twice came from behind to lead Turkey 3-2 before Leicester's Cengiz Under made it 3-3.