The Mexican, who led his country at the 2010 World Cup finals in South Africa, had been in charge of the Aragon club since November of the same year.
Zaragoza are bottom of La Liga, having lost eight of their last nine league games.
A statement on the club's official ebsite www.realzaragoza.com read: "Late last night on Thursday, December 29, Real Zaragoza reached an agreement with Javier Aguirre for the termination of his contract as first-team coach."vAguirre succeeded Jose Aurelio Gay at the helm and managed to keep the club in the top flight last season as Zaragoza finished two points clear of relegated Deportivo La Coruna in a closely-fought relegation scrap.
However, the first half of the season indicated the team would struggle to avoid the drop this time around and the club admitted in their statement that they felt it was time for a change.
"Real Zaragoza wishes to acknowledge the professionalism and dedication displayed by Javier Aguirre during the time he has been coaching the team," the statement continued.
"However, the sporting situation that faced the team required an urgent change of direction, so it has come to this agreement.
"Real Zaragoza wishes Javier Aguirre every success in his future career. We would also seek to highlight the exemplary attitude he has shown during his stay."
The 53-year-old, who played for his country when they hosted the 1986 World Cup, also led Mexico as coach at the 2002 finals in Japan and South Korea.
Prior to his second spell as Mexico coach, he was in charge at Osasuna between 2002 and 2006 before moving on to Atletico Madrid between 2006 and 2009.