The club have experienced a tricky 24 hours after Ángel Correa and Sime Vrsaljko tested positive for the virus on Sunday.
Atletico feared they could have infected other players but Monday’s results all came back negative and eased the fears about Thursday’s game against RB Leipzig in the Champions League going ahead.
Correa and Vrsaljko are asymptomatic but remain at home isolating.
Their families, per protocol, were also tested for coronavirus but all returned negative results.
Atleti trained on Monday with 21 available first team players plus academy players Alex Dos Santos, Manu Sánchez, Riquelme and Toni Moya.
They will then fly to Lisbon for the final eight of the Champions League on Tuesday morning.
The original plan had been to fly on Monday night but the coronavirus scare has forced the La Liga club to change their plans.