The reclusive Watterson stopped drawing Calvin and Hobbes after about 10 years in 1995 and not much has been seen from him since.
Pastis, a big fan of Watterson's, was able to lure the elder artist into working with him after making some references to the classic comic strip in his own strip.
"Let me tell you. Just getting an email from Bill Watterson is one of the most mind-blowing, surreal experiences I have ever had. Bill Watterson really exists? And he sends email? And he's communicating with me?" Pastis wrote on his blog.
"But he was. And he had a great sense of humor about the strip I had done, and was very funny, and oh yeah.... He had a comic strip idea he wanted to run by me."
The two collaborated on three strips of Pearls Before Swine, not revealing the fact that Watterson was involved until after all three strips had run.
The premise is that Pearls Before Swine was taken over for three strips by a 2nd-grader, Libby, or Lib, who had better drawing skills than Pastis.
Pastis said the three original panels of the strip Watterson drew would be auctioned off for charity.