Ripa, 49, and Seacrest, 45, sat at two separate tables that were pushed together in order to maintain a safe distance of at least six feet.
In order to fit both hosts in a screen, the producers used a split visual for them to appear side by side.
There was no in-studio audience for the ABC show.
“It’s gonna be a minute because we are used to shooting the show through a computer screen," Ripa said during their first broadcast back.
Seacrest added: “When we started going through our computer screens at home, I got so used to it, I forgot how to do this.”
Ripa then gushed on her reunion with Seacrest, saying that since he joined as her co-host in May 2017, the time has “flown by.”
"I have missed you very much," the “American Idol” host responded.
After the broadcast, both Ripa and Seacrest shared photos of their new normal on set.
The radio personality posted a photo of Ripa and he socially distanced with the caption, “Back in studio with new seating charts. Shout-out to everyone working behind-the-scenes to keep us safe and healthy. See you again tomorrow!"
Ripa posted an image of her “Live” co-host and she in hazmat suit standing next to each other.
"Guess who’s back in the studio today?" the former soap star wrote.
Over the past few months, the talk show hosts have been hit by trolls over their appearance during their virtual show.
Last month, the pair posted a promo video for the new upcoming season, which featured Seacrest and Ripa appearing to robotically get through their morning routine for the promo before returning to set.
"The only issue I have with this show (and I watch daily since I am at home nowadays) is the lack of personal grooming," one person commented under Ripa’s post. "I mean it’s a nationally televised show. And I have to get dressed for every Zoom work call so why can’t you guys?"
Ripa shot back: "I’ll bring it up at the next meeting."