Ballack had signalled the two Group Four qualifiers against Liechtenstein and Wales would be a fresh start for the Euro 2008 finalists after months of internal wrangling and consecutive home defeats in friendlies against England and Norway.
While Germany won both matches, the row on the pitch in Cardiff showed peace had yet to return to the squad since Ballack publicly fell out with coach Joachim Loew after the Euro 2008 final defeat against Spain.
On Wednesday, Podolski challenged a Ballack tactical order in the 67th minute with the score already 2-0, before pushing his captain away. Two more players rushed in to separate them.
Germany manager Oliver Bierhoff was quick to dismiss the incident, saying the air had been cleared immediately after the match.
"They looked deep into each other's eyes and the matter was dealt with," Bierhoff told reporters on Thursday, ruling out any punishment for Podolski.
Ballack, backed by Loew, said Podolski had disagreed with a tactical decision.
"Lukas still has a lot to learn. If he has a different opinion then we can discuss it off the pitch. But he has to accept the captain's decision on it," Ballack told ARD television.
"And in no way should he get physical," Ballack said of being pushed by the striker following the disagreement.
This is not the first sign of simmering differences with Ballack. Striker Miroslav Klose recently said the Chelsea midfielder had changed, getting closer to players and appearing more open.
Ballack said he was no different to before the row last year that saw him briefly out of the squad.
Despite the discord Germany, still have a near-perfect 2010 World Cup qualification record, topping their group with 16 out of possible 18 points after six matches, four ahead of main competitors Russia, who have a game in hand.
