Lahm found himself in trouble for a newspaper interview in which he criticised the club's transfer policy.
Toni incurred Bayern's wrath after driving home at halftime following his substitution in their 1-1 draw against Schalke.
Lahm had a meeting with club management on Monday and Bayern said they had closed the matter after receiving an apology.
"Lahm apologised for his comments in a very open, long and constructive discussion," the club said in a statement.
Following the earlier announcement of the fines, Bayern had said they were disappointed by the players.
"We are disappointed because as a substitute captain (Lahm) has a special responsibility for the team and club," said general director Karl-Heinz Rummenigge. "So Philipp Lahm is fined a record amount never seen before at Bayern."
Toni, unhappy with his treatment under coach Louis van Gaal, has been fighting for a starting spot hoping to get matches under his belt and make the Italy squad for the 2010 World Cup in South Africa.
"By leaving without any permission, Luca Toni showed an unacceptable loss of discipline," the club said in a statement.
Bayern have failed to hit top form this season and are eighth in the Bundesliga after 12 matches, while on the brink of a first round exit from the Champions League.
