Keisuke Honda's scored in the first-half via a penalty to put his side three points clear on top of Group D after two matches.
Japan played well and dominated the game hitting the post on a few occasions, plus good defending helped make the outcome look closer than it really was.
"It was a very complicated game because Iraq defended well and we couldn't penetrate," Aguirre told reporters after the game.
"We had chances to score more goals and couldn't convert, but we took three points and didn't pick up any injuries so I'm very happy."
Aguirre confirmed that the Brisbane heat effected his players towards the end of the game but felt that it would not affect them going forward in the tournament.
"There was some fatigue towards the end," conceded Aguirre. "But the players did well. Luckily we got into a nice rhythm early on," he added.
Iraq coach Radhi Shenaishil said that lack of preparation did not help their cause.
"We didn't have enough time to prepare for this tournament," he said. "We did our best to get the players ready, but they haven't reached the level where they can play a full match.
"Look at Honda," the Iraqi coach added. "He comes from the Italian league straight here, he's ready. We have players who haven't played since the Gulf Cup (last November)."
Japan are favourites to reach the quarter-finals with Iraq after the final round of group games against Jordan and Palestine respectively.