It formally ends the 10 year long tenure of John Momis.
Toroama will now head a small caretaker team until all the MPs elected in the August election within the automous region in PNG, are also sworn in, late next week.
Once a freedom fighter with the Bougainville Revolutionary Army, Toroama is seen by many as the ideal person to complete the region's quest for independence.
Australian peace activist Vikki John, for one, was delighted with his victory.
"I am over the moon that Ishmael Toroama is the new President of Bougainville. Congratulations to Ishmael and congratulations to the people of Bougainville," she said.
"This is exactly what Bougainville needs to get their independence that they have been waiting for a very long time."