Pecker is a key witness in the case against the former US president, who is accused of falsifying business records to cover up hush-money payment
The team announced the two positive tests on Sunday but had not identified who was infected.
It said the entire squad was re-tested and results came back negative for everyone else on Monday.
Atletico will face Leipzig on Thursday. It will be traveling to Portugal on Tuesday.
The last eight is scheduled to begin in Lisbon on Wednesday amid tight health safety protocols to prevent a coronavirus outbreak from derailing the competition's finale. The semifinals and Aug. 23 final will also be played in Lisbon.
Other clubs involved in the quarterfinals have not reported any positive tests among its players recently.
Pecker is a key witness in the case against the former US president, who is accused of falsifying business records to cover up hush-money payment
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