He called it "crazy" that anyone would make up such a story.
The paternity suit was filed in San Diego Superior Court by Maria Yeater. She had just turned 19 when she says she and Bieber, then 16, had a brief sexual encounter after one of the singer's concerts last fall.
Los Angeles police have said Yeater could be investigated for having had sex with a minor.
Bieber, on hand to promote a Christmas album, returns to "Today" to perform live Nov. 23.