The defender picked up the problem during Real's 1-1 draw with Real Valladolid on Wednesday and was sent for tests to determine the extent of the problem.
On Friday, the club announced Pepe had suffered a "grade one" injury which could reportedly see him sidelined for up to two weeks, meaning he would face a race against time to be fit for the European final in Lisbon on May 24.
"After receiving imaging tests today, the Real Madrid player Pepe was diagnosed with a grade one injury in the calf muscle of his left leg," the club statement read.
"The player's progress will be monitored."
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