His first guest, Chris Rock, asked Cooper why he was hosting "Live With Regis and Kelly" instead of covering hurricanes and floods as he usually does for CNN. Rock said "you're the disaster guy!"
Cooper will be followed by a series of fill-ins, including Howie Mandell, Pat Sajak, Jeff Probst and Donald Trump. Philbin is expected to be out five weeks.
Kelly Ripa says Philbin has received "thousands" of get-well e-mails on the show's Web site, including one that suggested that he save the plaque that will be removed from his arteries and give it to Ripa.
Philbin made the announcement about his surgery live on the show Monday.
"Well, listen, I gotta tell you something. ... I had been feeling chest pains, you know, and, uh, shortness of breath and all those little symptoms that you hear about," Philbin, 75, told his TV audience. After a number of tests, doctors recommended bypass surgery.