"I made a little mistake in there and couldn't get it back again. It was a stupid mistake," said Khan.
"That's boxing. One punch can change the fight. I'm fine but I need to go back to the drawing board and put it right.
"I'm a world beater and I'm going to come back stronger. I'm really sorry to my fans."
Before the fight Khan said he had been working on his much-criticised defence with new trainer Jorge Rubio, but Prescott rocked the Bolton fighter within seconds of the start.
When Khan went down for a second time the referee called the bout off
A stiff jab snapped Khan's head back and he was soon caught by a crisp left hook.
Khan managed to absorb a right hand but was then caught by a second left hook from Prescott and his legs buckled before he hit the deck.
It looked as though he would struggle to beat the count as his legs threatened to go from under him, but he managed to convince the referee he was fit to continue after taking a full eight count.
But when the bout resumed he immediately walked onto a right hand from Prescott and another right and left from the Colombian was enough to send Khan crashing and ruin his unbeaten record.
It was Khan's first fight on pay per view television and his first bout since starting to work with Cuban trainer Rubio.
Khan's promoter Frank Warren said he took responsibility for putting him in the ring with the dangerous Prescott.
"I've got to take responsibility for it," said Warren.
"This guy was recommended by the new trainer but ultimately I take responsibility and it's back to the drawing board.
"He was caught cold. We knew this guy was a dangerous puncher. He's not the first fighter to be beat and come back to win world titles. It's how you come back from it."
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