"There will be no more football on Mondays. As of next season, football will be on Saturday and Sunday. Business is important but fans are more important," Rubiales said in a post on his personal Twitter account.
Spanish top flight games have been played on Mondays since 2010 and while the league's organising body says the matches have large television audiences, they have led to a fall in attendances.
Alaves supporters staged a high-profile demonstration against Monday games last month at their match at home to Levante, keeping the stadium empty until five minutes after kick off, while a small group held a mock funeral inside the ground marking "the death of modern football".
Rubiales said the federation was also in discussions about ending games on Fridays, although he did not confirm whether they would also be discontinued.
"We'll see what happens with games on Friday, perhaps we can come to an agreement that is good for everyone," he added.
Spain's biggest clubs such as Real Madrid, Barcelona, Atletico Madrid and Sevilla are not required to play on Mondays or Friday due to being involved in European competition.
The rule has led to some clubs playing a disproportionate number of times on Monday, such as Athletic Bilbao, who have played eight out of 25 fixtures this campaign on Monday.
(Reporting by Richard Martin; Editing by Toby Davis)
