Hibs slipped down to the second tier on Sunday as they lost their playoff against Hamilton Academical on penalties.
Manager Terry Butcher held individual meetings with his squad on Monday morning, and McPake and Thomson were among those who were told that they will not be offered new contracts next season.
"The manager has told me I'll not be part of his plans," McPake told Sky Sports News. "The blame lies with the players as we got the club relegated but you cannot look entirely at the players.
"I'm gutted. I love playing for this football club. It was some good and some very bad times as well but I'm more disappointed I never got the chance to help the club stay in the division."
Hibs were last relegated from the top flight of Scottish football in 1998, but they managed to gain promotion the next season.