Obama said the volunteers' actions were "unacceptable and in no way reflect any policy of my campaign".
"I take deepest offence to and will continue to fight against discrimination against people of any religious group or background," he said.
The two women issued a statement saying the "incident was unfortunate and extremely disappointing."
However they said that they appreciated Obama's apology and said they would continue to support his presidential campaign.
"The infringement on our rights occurred and has been addressed; now we are ready to move forward."
His personal apology followed an earlier apology made to the women by his campaign staff.
The Council on American-Islamic Relations (CAIR), a US Muslim group, urged candidates from parties not to give in to pressure from groups that sought to stigmatise Muslims.
"We welcome the campaign's apology and urge candidates of all parties not to give in to pressure from the vocal minority of Islamophobes in our society that seeks to stigmatise Islam and marginalise American Muslims," Corey Saylor, a CAIR director said.
"All presidential campaigns need to clearly answer the question: Should American Muslims be marginalised from their country's political process simply because of their faith?"