Barca this week let Suarez leave for Atletico in a €6million deal, with new head coach Ronald Koeman having told him he was surplus to requirements.
Koeman's treatment of the former Liverpool star was believed to be one of the motivating factors behind Messi's desire to force a sensational exit from Camp Nou, but he said president Josep Maria Bartomeu made a move "impossible" by going back on his word to let him leave for free.
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.
Suarez is the third-highest scorer in Barcelona's history with 198 goals and won 13 trophies, including four LaLiga titles and the 2014-15 Champions League, during a six-year spell with the Catalan giants.
Messi was angry with the way things ended for Suarez but said "at this point nothing surprises me".
"I was already getting the idea but today [Friday] I entered the dressing room and the penny really dropped," Messi wrote on Instagram alongside a photo of him and Suarez following the latter's farewell news conference on Thursday.
"It is going to be so difficult to not continue sharing the day to day with you, both on the pitches and away from them. We are going to miss you so much. It was many years, a lot of [yerba] mate, lunches, dinners… many things that will never be forgotten, all those days together.
"It will be strange to see you in another shirt and more so to face you. You deserved to leave 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 did. But the truth is that at this point nothing surprises me.
"I wish you all the best in this new challenge. I love you very much, we love you very much. See you soon, friend."
Suarez followed Ivan Rakitic, Arturo Vidal and Nelson Semedo as the latest high-earning figure to be moved on by Barca ahead of the 2020-21 season.