The World Player of the Year was part of the Argentina squad that Maradona led to the quarter-finals of the World Cup in South Africa a month ago before the former captain was let go by the Argentine FA last week.
"I certainly did not want him to leave, I hoped he would stay," Messi told a news conference ahead of the Spanish champions' pre-season friendly against Beijing Guoan on Saturday.
"But this is football. There are always many uncertainties."
Messi also made his feelings plain about Barcelona transfer target Fabregas, who is reported to be angling for a move away from Arsenal and back to his home city.
"I'm very much looking forward to playing with Fabregas as part of the same team one day," he said.
Barcelona face the Chinese champions in the Bird's Nest stadium on Saturday, exactly two years after the spectacular opening ceremony kicked off the Beijing Olympics.
The 23-year-old has good memories of the stadium having won Olympic gold with the Argentina under-23 team in a final victory over Nigeria in the 90,000-seater arena two years ago.
The match will be Barcelona's second match on their tour of Asia after the 5-2 victory over a South Korean K-League All Stars side in Seoul on Wednesday.
Messi came on after half an hour and quickly found his scoring touch with two goals in the last three minutes of the first half before sitting out the second period.
His appearance was the subject of some controversy with pressure from the match promoter forcing manager Pep Guardiola to reverse his decision not to play Messi, who had just returned from holiday.
Guardiola, who is without his eight Spanish World Cup winners on the Asian tour, said Messi would definitely get on the pitch on Saturday and the player himself was eager to turn out.
"As a player I always want to play," he said. "There is no problem with my physical condition and I haven't had any problems in training."
