Coached by former Villarreal boss Manuel Pellegrini, ambitious Qatar-owned Malaga took the lead in the fifth minute at their Rosaleda stadium when Frenchman Toulalan nodded in from a corner.
Villarreal's Argentine striker Marco Ruben, filling in for sidelined first-choice pair Giuseppe Rossi and Nilmar, levelled in the 16th minute when he finished off a swift breakaway with a powerful drive high into the net.
Isco netted what proved to be the winning goal after he played Venezuela striker Salomon Rondon through five minutes before half-time.
The 19-year-old midfielder followed up on Rondon's saved effort to poke the ball past Diego Lopez to give Malaga their fourth win in five matches.
Toulalan was shown a second yellow card with around 15 minutes left for a foul on the edge of the home penalty area and former Spain international Marcos Senna curled the ball against the bar from the resulting free-kick.
Leaders Real Madrid moved six clear of great rivals Barcelona on 34 points at the weekend after Jose Mourinho's side thumped city rivals Atletico 4-1 and champions Barca suffered their first defeat of the campaign at Getafe, losing 1-0.
Valencia are third, a point behind Barca, after a 2-1 win at Rayo Vallecano, with surprise packages Levante a further point back in fourth thanks to a 4-0 success at home to Sporting Gijon.
Malaga are three points behind Levante and Sevilla, who won 1-0 at Real Zaragoza, are two behind in sixth.
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