The American beat him on a unanimous points decision in Las Vegas early this morning.
Commentators said it was an easy fight for Mayweather who dominated throughout .
But Christian Pacquiao fought back hard in the fourth round when he landed a big shot from his southpaw stance.
In his post-match interview he said he thought he had won.
The Filipino had said the glory would belong to God if he beat Mayweather.
Pacquiao has previously spoke of his Christian faith.
"I have a lot of dreams and visions," he told the Guardian, "I even heard the voice of God. When I heard the voice of God, I am trembling and melting. I feel I have died. It was an amazing, amazing experience.
"I'm happy because I found the right way, salvation, born again. We are required to be born again, all of us.
"Christ said unless we are born again we cannot enter the kingdom of God. So it's very important to me.
"Jesus Christ said: 'I am the way and the truth and the life. No one comes to the Father except through me.' There is no other way. The only way is through Jesus."
The boxer had been seen as the 'bad boy' of the sport until a few years ago.
"People are surprised by the way I have changed my life," he said.
"I knew I could do whatever I wanted. But I changed when I heard the voice of God, and I can testify that there is a God.
"I saw two angels, white, long, big wings. I saw Paradise. God showed me about the end of time. This all happened within the last three years. That's how I changed my life."