The 37-year-old television personality will join Hoda Kotb as co-host of the show's fourth hour following Gifford's departure in April.
Hager announced the news alongside Gifford and Kotb during Tuesday's episode of Today.
"Jenna Bush Hager has been filling in on this show for years," Kotb said. "Here at NBC and around the country, Jenna is loved."
"I can't believe it," Hager said. "It feels humbling and I can't believe it."
Hager said she wept after her dad, former president George W. Bush, told her he was "very proud" of her new gig. She had nothing but praise for Gifford, who has co-hosted the fourth hour with Kotb since 2008.
"Obviously you have been such a role model and so generous with your time," Hager told Gifford. "You are beloved here in so many ways. And if I can use some of your grace and have half of what you've done, my life will be a very happy one."
Hager joined NBC as a Today correspondent in 2009. Gifford announced plans in December to leave Today, calling her impending exit "bittersweet."
"I've been in this business 120 years and I've never worked with a more beautiful group of people," she said on the show. "You're just so special, Hoda. Thank you so much."