Riverdale executive producer Roberto Aguirre-Sacasa made the announcement at San Diego Comic Con on Sunday.
Aguirre-Sacasa said Doherty will appear on the episode scheduled to air on Oct. 9.
He did not offer details about the character she will play other than to say it will be a "special role."
"They were such good friends, and when we were putting together this tribute episode, we wanted to make it as special as possible, and so we asked Shannen to do a pivotal, super-emotional role. She read the script and immediately said 'yes.' It's very impactful," Aguirre-Sacasa said.
"I am deeply honored to pay tribute to Luke on Riverdale. The care in which this show takes in honoring his memory is beautiful. He is missed. Today. Tomorrow. Forever," Doherty wrote in an Instagram post.
Perry played Fred Andrews, the father of central character Archie Andrews (KJ Apa,) on Riverdale.
Perry died on March 4 after suffering a stroke. He was 52.
Riverdale is The CW's adaptation of the Archie Comics series. It co-stars Lili Reinhart, Camila Mendes, Cole Sprouse, Marisol Nichols, Madelaine Petsch, Mark Consuelos, Casey Cott, Charles Melton, Vanessa Morgan, Skeet Ulrich and Mädchen Amick.