The United Arab Emirates team overturned a 2-1 first-leg deficit, with Soufiane Rahimi and Kodjo Laba both scoring twice and Kaku also on target against a Marinos team for whom Yan Matheus scored and goalkeeper William Popp was sent off.
Al Ain, who last won the title in 2003, levelled the aggregate score in the eighth minute, Rahimi slotting home after latching onto Yahia Nader's clever back heel and, by the 33rd minute, the home side had taken the lead in the tie.
Rahimi was involved again, the Moroccan brought down by Shinnosuke Hatanaka to allow Paraguayan playmaker Kaku to step up and score from the penalty spot.
Seven minutes later, however, Marinos struck when Khalid Eisa was unable to do enough to palm Matheus' low shot to safety and the aggregate score was level again.
Marinos's task became more complicated deep into first half injury time when Popp was sent off for bringing down Rahimi as the Moroccan raced towards goal.
Rahimi then hit Al Ain's crucial third in the 67th minute as he capitalised on the inability of the Marinos defence to clear, beating substitute goalkeeper Fuma Shirasaka with a left-foot shot inside his near post.
Substitute Laba struck twice after his late introduction - in the 91st and 95th minutes - following more poor defending to put the seal on a remarkable win.
