Vida returned a negative test on Monday but another test conducted earlier on Wednesday ultimately proved to be positive.
The former Dynamo Kyiv defender was substituted at half time in a game that ended 3-3 at the Vodafone Park in Istanbul.
The 31-year-old Besiktas defender has been placed in self-isolation and will miss Croatia’s upcoming UEFA Nations League games against Sweden and Portugal.
'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,' a Croatia Football Federation statement read.
'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 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.'
Vida has been capped 84 times by Croatia and was part of the side that reached the final of the 2018 FIFA World Cup, losing 4-2 to France.
