Iran took the lead in the 16th minute with a penalty from Ashkan Dejagah after a wild, sliding challenge from Jan Vargas on Karim Ansarifard.
Three minutes later, Saman Ghoddos doubled Iran’s advantage.
It was Ghoddos’s first goal in his third match for Iran national football team.
Panama pulled a goal back in the 39th minute, also from the penalty spot, with Gabriel Torres converting after Rouzbeh Chesmi was harshly ruled to have fouled Armando Cooper.
Iran will be playing in its fifth World Cup next year in Russia while Panama has qualified for the first time.