The positive cases were discovered after players and club staff travelling to Lisbon were tested in Madrid on Saturday.
The Spanish club said the individuals are isolating at home. They will be retested along with close contacts of the positive cases.
“This motivates changes in the training schedules, in the structure and development of the trip and the accommodation in the Portuguese capital,” Atletico said in a statement.
“The club will coordinate the new schedules with Uefa and as soon as there is a new plan it will be made public. It also calls for maximum respect for the identity of the two positive cases.”