The former GMTV anchor had been tipped as a possible new host of the breakfast show, amid speculation that Christine Bleakley and Adrian Chiles will leave the programme within weeks.
However, Holmes has confirmed on his official website that he will not make a return to ITV, instead deciding to continue with Sky News's Sunrise.
"Being so associated with breakfast television for so long, there is often speculation linking me to other vacancies when they occur," he said.
"I have had a really exciting, fulfilling and happy six years at Sky News and with today's signing of a new contract, I am delighted to continue hosting Sunrise with Eamonn Holmes for at least another three."
"But it is also a great privilege for me to work with colleagues who I not only respect, but like so much. There is no doubt our off-screen friendship shines through on screen."
Adding that he and his team "try to serve up the daily news and sport agenda in a fast, professional yet often fun way", the broadcast added that Sky News is "simply the conduit for top news professionals in the field and our role is to do them and our newsroom colleagues justice in relaying the stories that make the world go around".
ITV has yet to confirm if Bleakley and Chiles will exit the show. Departing BBC Breakfast host Sian Williams has also been linked to a role, should the current duo be replaced.
> Eamonn Holmes, Ruth Langsford: 'Hosting This Morning is exciting'