Mrs Rooney gave birth to Klay Anthony Rooney at 2.11am.
Just hours later she tweeted the good news to her one million Twitter followers, saying: "At 2.11am our Beautiful Son... Klay Anthony Rooney entered the world. He weighed 7lb 11 1/2 oz. We're all so happy and doing well. X"
Rooney also tweeted: "Both Klay and Coleen are fine... We're all delighted!"
Mrs Rooney reportedly went into labour over the weekend, complaing on Saturday that she had experienced an uncomfortable night's sleep.
She tweeted: "#hurryupbaby Looks like its gonna be a nice day today!! Enjoy x"
Klay is the younger brother to the Rooneys' first son, Kai, three, who was born on November 2, 2009.
The couple, both 27, married on June 12, 2008 after meeting at secondary school.
Rooney missed Manchester United's last game of the season against West Bromwich Albion on Sunday to be with his wife.