The striker has suffered a grade one hamstring injury and is unlikely to be fit for Saturday's clash with Real Madrid in Lisbon
The Spain international was susbtituted early on during his side's 1-1 draw with Barcelona last Saturday and was reduced to tears whilst receiving treatment on the sidelines.
The club have since confirmed he has suffered a grade one hamstring injury, throwing his chances of playing against Real Madrid into serious doubt, whilst also raising concerns over his availability for the World Cup starting next month.
"Diego Costa has suffered a grade one muscular injury to the femoral bicep of the back of his right leg," the club tweeted through their official account, before confirming they are waiting for definitive news on the length of time needed for the striker's recovery.
Costa - who is widely expected to join Chelsea in a €42.5 million deal this summer - has scored 36 goals in all competitions as Atletico soared to an historic La Liga title as well as a place in the Champions League final.
The Brazil-born star was struggling with a hamstring problem prior to Saturday's Liga decider at Camp Nou, but head coach Diego Simeone had insisted the player was ready to play following training during the week.