The ban, which follows a similar edict in neighboring Malaysia, was passed after investigators visited gyms and private yoga classes across the country to see what effect Hindu rituals like chanting mantras might have on Muslims.
Amin said clerics decided it could weaken their faith.
"Those who perform yoga purely for health reasons or sport will not be affected," he added. "We only prohibit activities that can corrupt Islamic values."
Indonesia is a secular country of 235 million people, 90 percent of whom are Muslim. Though most practice a moderate form of the faith, a vocal extremist fringe has gained strength in recent years.
In recent years, yoga -- a blend of physical and mental exercises aimed at integrating mind, body and spirit
-- has been increasingly practiced in gyms and dedicated centers around the world.
In the United States, where it has become so popular that many public schools began offering it in gym classes, yoga has also come under fire.
Some Christian fundamentalists and even secular parents have argued that yoga's Hindu roots conflict with Christian teachings and that using it in school might violate the separation of church and state.
Egypt's highest theological body also banned yoga for Muslims in 2004.
Indonesia's Ulema Council -- which wrapped up its annual meeting for the issuing of fatwas late Sunday
-- decided to investigate the need for a yoga ban after Malaysia's top Islamic body issued its fatwa late last year.