The Japanese side had won the first leg 2-0 in Kashima last week with Brazilian duo Leo Silva and Serginho on target.
That left Persepolis, also chasing their first continental title, with plenty to do in Tehran and although they created several chances in front of a 100,000-strong crowd at the Azadi Stadium, Go Oiwa's men held on to their two-goal advantage.
Kashima's triumph was the second straight time a Japanese team had won the title, following Urawa Red Diamonds' victory last year. Before that Gamba Osaka had claimed the crown in 2008.
Persepolis, known for their mean defence, had no option but to attack on Saturday, but Kashima goalkeeper Kwoun Sun-tae put in a virtuoso performance.
Kwoun, for whom this was a third Asian crown following two with South Korea's Jeonbuk Hyundai Motors, was at the top of his game, keeping the Iranians, especially Ali Alipour and Bashar Resan, at bay.
Seven minutes before half-time Resan muscled his way past two defenders close to the Kashima goal, but failed to beat Kwoun at his near post.
Persepolis coach Branko Ivankovic sent on Mohsen Rabiekhah and Ehsan Alvanzadeh in a desperate attempt to break the deadlock but to no avail.