He was taken to hospital after being substituted at half time in the 3-1 defeat by the United States on Saturday having tweaked his neck trying to head the ball but got the all-clear.
Cahill did not train fully with the squad on Tuesday, raising doubts over whether he would be fit to play on Sunday.
Team spokesman Rod Allen said Cahill sat out some of the morning session but was expected to take part in the next session later on Wednesday.
"He's fine, he's not injured... he just had a sore neck," he said of Cahill, who scored after 19 minutes against the U.S.
Losing the midfielder for the Germany match would have been a big blow because he is the main goal threat for a team that failed to convert a string of good chances in the second half against the Americans when he was off the field.
Forward Harry Kewell is back in full training after recovering from the groin strain he picked up earlier this year with his Turkish club Galatasaray.
Australia will also face Ghana on June 19 and Serbia four days later.
