Wiig bowed out of the comedy show after seven years on the recent season finale.
Co-hosting Live With Kelly, Meyers described the episode as "very emotional" and suggested that Wiig is "one of the best cast members" the show has seen.
"It was really sad," he added. "I mean, you spend every second with these people for seven years. It's like going to high school and college with them, minus a year!"
Questions have also been raised about the future of other Saturday Night Live stars, such as Jason Sudeikis and Andy Samberg, but Meyers admitted that he would like everyone to stay.
"But I feel like that's their decision to make," he said. "I want everybody to stay forever - it's such a great place to work. Someone recently said when you get hired at that place, it's like you get into Hogwarts - that's what Andy Samberg referred to it as - because you go to that place and all of a sudden everyone is just like you and you just laugh all the time."
Meyers also pointed out that it is "exciting" to introduce new cast members and suggested that he has no immediate plans to exit the show himself, saying: "I'll have to leave at some point because everybody does, but it's the most exciting job and I'm never bored."
Fred Armisen recently revealed that he would like to return to Saturday Night Live.