Speaking for the first time on Guardiola's exit, the Argentina forward said he was saddened to witness the end of the 41-year-old coach's four-year reign, which delivered an astonishing 14 major trophies - the last of which came with victory in last weekend's Copa del Rey final.
Messi remains optimistic, however, that Guardiola's assistant Tito Vilanova will be able to keep the good times rolling as he takes on one of the biggest jobs in world football.
"I was surprised and saddened by Guardiola's departure after four great years together with many titles," Messi told AS after arriving in his homeland to prepare for a World Cup qualifier against Ecuador.
"It won't be easy after all that Pep achieved, but they did everything together and Tito was a great help in these years."
Messi is coming off the back of an incredible season after netting 73 goals in all competitions - 50 of those coming in La Liga alone - but admitted he is still bothered his missed penalty that contributed to Barcelona's elimination from the Champions League at the hands of eventual winners Chelsea.
"We were close to winning the league and the Champions League," he said.
"I am madder about the Champions League because I think our elimination was unjust and also for missing that penalty. But this is already behind us.
"I am very happy for all the goals that I scored. My objective is the same every year - to keep learning, growing and improving."