Atletico Madrid say forward Angel Correa and defender Sime Vrsaljko tested positive for coronavirus before Thursday's Champions League quarter-final against RB Leipzig in Lisbon.
The players are isolating at home and will miss the rest of the tournament.
The two positive cases were discovered after players and staff travelling to Lisbon were tested in Madrid on Saturday.
Players and staff have since been retested with all results negative.
Relatives of Argentina winger Correa, 25, and 28-year-old Croatia right-back Vrsaljko were also tested and cleared.
The club said they decided to name the players to put an end to "speculation".
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The first team returned to training on Monday and the club said Correa was "asymptomatic and self-isolating at home", while Vrsaljko "was recovering from an injury and not training with the group".
"The Croat is also asymptomatic and will remain at home by decision of the medical services, although his case is considered to be resolved by the health authorities, having generated antibodies several months ago," Atletico said in a statement.
Because of the coronavirus pandemic, the Champions League is concluding with a 'final eight' tournament in Lisbon, with single-leg games held behind closed doors.