The newly-rich Andalusian side have set their target on upsetting the old order in the Spanish top flight following investment from Qatari Sheikh Abdullah Al Thani and currently lie in fifth place after a hard fought win.
Malaga have won every match at La Rosaleda so far this season except for the visit of Real Madrid and started well with French midfielder Jeremy Toulalan scoring a rare goal after four minutes.
Villarreal were on the back foot but equalised through Marco Ruben after a fine run from Borja Valero.
The visitors came more into the game as the first half continued but five minutes from the break Malaga got what proved to be the decisive goal through Isco Alarcon after an initial shot from Jose Rondon had been saved by Villarreal ‘keeper Diego Lopez.
Villarreal, who haven’t won away since beating Athletic Bilbao eight months ago, rallied and the hosts were reduced to ten men when Toulalan was shown a second yellow card.
Then, on 76 minutes, Valero saw a shot tipped onto the cross bar but there was no way back for the visitors.
Barcelona crashed to a shock 1-0 defeat at Getafe on Saturday and now trail Real Madrid, who came from a goal down to beat nine-man derby rivals Atletico Madrid 4-1, by six points.
It was the first defeat of the season for the reigning Spanish and European champions as Getafe frustrated their illustrious visitors, grabbing the three points thanks to a second half header from Juan Valera.
Barcelona’s last defeat came on April 30 when they lost 2-1 at Real Sociedad while Saturday’s drama added an extra edge to the first Clasico meeting in the league between Madrid and Barcelona, which takes place on December 10.