The TV presenter confirmed the news on Twitter on Monday night.
She wrote: "I'm sooo happy to tell you all - we've just had a baby boy! Chester William Baldwin made a grand entrance at 8lbs 12. He's just perfect. X"
Chester is the 33-year-old's third child with husband Dan Baldwin after daughter Belle and son Harry.
Stars congratulated her about the news, including Amanda Holden, who has replaced Willoughby on ITV's This Morning.
She tweeted: "Congratulations and much love to @hollywills Dan Belle Harry and new baby Chester !!I'm delighted and thrilled!!"
Swimmer Rebecca Adlington wrote: "Congratulations!!!! Amazing."
The Saturdays singer Rochelle Humes said: "How lovely. Congrats to you and Dan."
This Morning host Willoughby left the ITV show earlier this month, before promising viewers she would return as she handed over to Holden in tears.
Willoughby admitted she had found it difficult to talk to co-host Phillip Schofield without welling up, saying she'd miss the programme and the team.
Her husband called the show, telling her: "We can't wait for you to come home, all of us - the kids are so excited.
"Have you made the announcement yet that we are having a baby girl? It's a girl everyone, it's a girl."
Willoughby told This Morning viewers that he was lying and said they still had no idea of the sex of the baby, telling them: "We really don't know.
"I'm going to miss you all. It's such a lovely show and I'll be watching."
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Holly Willoughby has given birth to her third child, a boy named Chester.