"He's recovering very well", the actor announced during his monologue on Wednesday night. "Jimmy told me today that the respirator is out", he said.
Harris noted that Billy is also eating and smiling.
"We're sending lots of love to all the Kimmels", Harris added.
Billy - who was born with Tetralogy of Fallot (TOF) with pulmonary atresia - was originally scheduled to have his second heart operation in late October, but it had to be postponed because the family were suffering from colds. "I'm so glad he's doing well".
Neil delivered the opening monologue for Jimmy during the show.
Kimmel's wife and head writer Molly McNeary talked to THR about why the couple shared their son's health issues on TV in this week's Women in Entertainment issue.
"So there I am, in my living room breastfeeding Billy with my mom beside me, and we're watching". I couldn't believe the strength that it took to tell that story a week after it happened. He didn't have to do that.
Little did McNearney or Kimmel realize, the remarks would strike quite a nerve in the public discourse as debate over health care was heating up at the same time.
Here's the "How I Met Your Mother" alum's best-received quip of the evening: "I'm what's known in Hollywood as a triple-threat: I sing, I dance, and I don't sexually harass people".
"I am the guest host for the night".
Despite having to endure heart surgery three days after his birth, McNeary found objective and hope in Billy's medical battles.
"Again, I didn't think much of it".
"If your baby is going to die and it doesn't have to, it shouldn't matter how much money you make". Guest hosts like Harris will be filling in for Kimmel. Last month, Jennifer Lawrence, Channing Tatum, Shaquille O'Neal and Dave Grohl subbed for Kimmel.