Suarez was told last month that he was surplus to requirements at Camp Nou, and he eventually left on Thursday to sign for Diego Simeone's Atleti.
Messi and Suarez were known to be good friends within the dressing room and it's clear that the Argentine, who himself flirted with a move away for much of the summer only to agree to remain last month, is not pleased with Suarez's departure.
His post on Instagram read: I was already getting the idea, but today I went into the locker room and I felt the truth, how difficult it is going to be not to continue sharing the day to day with you, both on the pitch and outside.
"We are going to miss you very much. It was many years, many mates, lunches, dinners ... Many things that never they will forget, every day together.
"It will be strange to see you with another shirt, and much more to face you. You deserved to depart like what you are, one of the most important players in the club's history, achieving important things both as a group and individually, and not to get kicked out like they have done. But the truth is that at this point nothing surprises me any more.
"I wish you all the best in this new challenge. I love you very much, I love you very much. See you soon, friend."
Messi's disgruntlement at the way the club is being run clearly hasn't gone away with his decision to remain, and this season could see the relationship between club and player disintegrate even further.
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Ya me venía haciendo la idea pero hoy entré al vestuario y me cayó la ficha de verdad. Que difícil va a ser no seguir compartiendo el día a día con vos, tanto en las canchas como afuera. Los vamos a extrañar muchísimo. Fueron muchos años, muchos mates, comidas, cenas... Muchas cosas que nunca se van a olvidar, todos los días juntos. Va a ser raro verte con otra camiseta y mucho más enfrentarte. Te merecías que te despidan como lo que sos: uno de los jugadores más importantes de la historia del club, consiguiendo cosas importantes tanto en lo grupal como individualmente. Y no que te echen como lo hicieron. Pero la verdad que a esta altura ya no me sorprende nada. Te deseo todo lo mejor en este nuevo desafío. Te quiero mucho, los quiero mucho. Hasta pronto, amigo.