Hoeness reprimanded Sammer for accusing the team of "lacking emotion" and "hiding behind the coach (Pep Guardiola)" in the wake of a 2-0 Bundesliga win over Hannover on September 14.
Hoeness branded the comments "unnecessary", insisting there was no need to be so critical after a comfortable win.
The pair have discussed the situation and Hoeness said on Tuesday it "was finished".
He was quoted as saying in the Bild newspaper: "He expressed his opinion, we express ours.
"We have talked to each other in the meantime and there's nothing more to say.
"If reasonable men sit down together, there are always sensible solutions.
"The coach is responsible for everything that goes on with the team and it should stay that way."
Bayern, who face Hannover again in the DFB-Pokal on Wednesday night, lie second in the Bundesliga table after six games, level on points with leaders Borussia Dortmund.