Spain's secretary of state for sport Miguel Cardenal oversaw the negotiations, which settled the numbers of games each company could show on their individual platforms each week.
Mediapro will continue to show one match on their free-to-air channel each week and will control the international rights for La Liga.
"The agreement establishes a viable model for the Spanish league and presents a stable scenario for football fans for the seasons 2012-13, 2013-14 and 2014-15," Mediapro said.
"The professional soccer league (LFP), for their part, guarantee the new agreement signed by both operators."
A group of 13 first division sides had forced a meeting with the LFP on Tuesday to call for a settlement of the dispute saying that it created "a situation of serious legal insecurity", and had threatened to postpone the season's start.