Mahboob took gold in a time of 2 hours, 12 minutes and 38 seconds, with Kohei Matsumura one second behind in second place, followed by Japanese teammate Yuki Kawauchi.
Mahboob is past winner of the Asiad 5,000 and 10,000 meters. Originally from Kenya, he changed his nationality to the Arab state in 2005.
His win comes days after Kenya's Dennis Kimetto set a new world marathon record of 2:02.57 in Berlin, raising the bar for distance runners worldwide.
"Slowly by slowly. Time will tell," he said.
Mahboob's win is the ninth athletics gold medal for tiny Bahrain at the Asiad, as the island nation continues its policy of nationalising athletes from other countries. It has not won gold in any other sports in the South Korean port city of Incheon.
On the second-to-last day of the Asian Games, China leads in the overall medal tally, with 142 golds. Host South Korea is second with 73 and Japan third with 46.