Though Vida, along with the rest of the team, had tested negatively on Monday, subsequent tests on the morning of the game resulted in a 'potentially positive result' being returned as the match was unfolding.
As a precaution, the 31-year-old, who plays club football for Besiktas, was taken off at half-time and put into immediate isolation with further testing confirming his positive Covid-19 diagnosis.
The Croatian Football Federation revealed the coronavirus scare post-match and were quick to stress that they had adhered strictly to all UEFA protocol.
"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," their statement read.
"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."
Croatia came from behind twice on Wednesday before themselves squandering a lead in a seesawing 3-3 draw.
"It was a really friendly match, with six goals, and I can be happy because I saw some things I wanted to see, but I can also be unhappy because we let in three goals lightly," manager Dalic said post-match.
"That worries me, it wasn’t good, our defence was weak. That must not happen."