The pair took the relaunched breakfast show's sofa spots formerly held by Kate Garraway and Dan Lobb, who were themselves the temporary replacements for original hosts Adrian Chiles and Christine Bleakley, who presented their final edition last December after being axed the previous month.
Jones opened the show by thanking viewers for choosing Daybreak, while Kelly described their arrival as "exciting" and likened the new-look studio to an "eternal summer".
"It's like the first day back at school isn't it?" she added. "And you're thinking about things all the time and you're worried the alarm is not going to go off."
Jones replied: "I had four alarms and I was checking them on the hour every hour. That's why I look like this ladies and gentlemen, I'm only 13."
The duo were joined by guests including James Nesbitt and Little Mix, who performed their number one single 'Wings'.
Signing off from their inaugural edition of Daybreak, Jones declared: "I've really enjoyed it, I'm exhausted. It's been really brilliant, it's been very busy hasn't it?
"But it's actually a great feeling welcoming everyone to the new family as well."
Kelly praised the Welsh singer for his efforts, saying: "It's been absolutely lovely, you're a joy, you absolutely are."
Gethin Jones and ex-GMTV star Richard Arnold joined the new presenting pair to provide features and entertainment news, while Matt Barbet and Ranvir Singh also made their first appearance hosting Daybreak between 6am and 7am.