Labruna resigned on Monday early morning after the club lost 1-2 against Huracan, which was the fourth defeat in five matches, the other match they tied.
Gimnasia is a team from the north of Argentina and it is in the drop zone for the second category.
Also Juan Manuel Llop resigned to coach Racing in the third match, Gustavo Alfaro resigned to coach Rosario Central in the fourth match.
Gimnasia's directive will offer the coaching to Hector Arzubialde, a former defender who played in the club and have coach inferior divisions.
Labruna, 51, had taken charge at the end of February 2008.