Zabaleta said that his side knew what type of game they would face and praised the quality of match-winner Messi, describing him as "the best player in the world".
"It was a difficult game and we knew it would be because Iran defended with practically 11 players behind the ball," the Manchester City defender told reporters.
"It was difficult to find spaces and they had two or three chances on the counter as well. That can happen because when we have the ball we try to attack quickly and in numbers - and sometimes that means we leave too many spaces at the back.
"When you have a player of Leo's quality who can pop up and be decisive, you always have a chance. We enjoy having the best player in the world and we know that he'll be there for us in a lot of situations when we need him, like today."
Argentina face Nigeria in their final group game on Wednesday.