"Yvon Neptune and Jocelerme Privert have been apprehended," said police spokesman Gessy Coicou on Saturday. "They are now in police custody at a secure location."
A police source had earlier said the prison housing the two officials was invaded by an armed group and a prison guard was shot in the head and killed.
Witnesses told police there was intense shooting after three vehicles approached the front of the prison at about 3.30pm (2030 GMT).
The dead prison guard's body lay in a pool of blood in front of the prison entrance as reinforcements of police and UN peacekeeping troops surrounded the facility.
The prison in the Haitian capital of Port-Au-Prince holds 1422 inmates, said human rights official Kettly Julien.
"There are many people who escaped but there are still prisoners inside," Julien said.
Aristide left Haiti in February last year amid an armed uprising and street protests against his rule. He now lives in exile in South Africa.
He was replaced by an interim government led by President Boniface Alexandre and Prime Minister Gerard Latortue.
A UN peacekeeping force was sent to Haiti last year but violence continues to plague the country.