Messi will miss Barca's La Liga matches at home to Sporting Gijon on Wednesday and at Athletic Bilbao on Saturday after he was felled by a late tackle from Atletico Madrid defender Tomas Ujfalusi at the weekend and sustained ankle ligament damage.
The World Player of the Year, who scored the opening goal in Barca's 2-1 win at the Calderon, is also doubtful for the Champions League match at Rubin Kazan on September 29.
"He (Messi) has some very special talents," Guardiola told a news conference. "He is almost irreplaceable but we'll move on and fortunately he's out for only a short time."
Guardiola said Messi could return in two or three weeks but Barca would not rush him back into action.
"I don't know if he'll make the Rubin Kazan game. He'll rest until he is well," the former Barca and Spain midfielder said.
The Spanish football federation's disciplinary committee sanctioned Ujfalusi with a two-match ban later on Tuesday, saying he had "acted dangerously causing injury".
The Czech, who was shown a straight red card for the challenge in added time, has apologised and said he did not deliberately hurt Messi.
"I am not a hard player," he told a news conference on Monday. "I go in hard but always going for the ball and I give my all in every game.
"There are harder tackles than the one on Messi. The problem is that I did mine on Leo Messi."
The former Fiorentina player was given backing on Tuesday by England's Italian manager Fabio Capello, who was in Madrid attending a UEFA conference.
"I know Ujfalusi very well and he's an honest player," Capello told reporters.
"I hope Messi returns very quickly because he's the kind of player it's always worth watching on the pitch."
