Sevilla were under pressure after Valencia beat promoted Real Zaragoza 3-1 earlier on Sunday to climb above the Andalusians but Mali striker Kanoute rose unmarked to nod in Adriano Correia's cross for a 66th-minute winner.
Valencia striker David Villa netted his eighth of the season against Zaragoza to move clear in the scoring charts ahead of Barcelona's Lionel Messi and Zlatan Ibrahimovic on seven.
Champions Barca top the standings with 26 points from 10 matches, with Real Madrid on 25 and Sevilla on 22. Valencia are a point behind Sevilla in fourth while Villarreal are down in 16th place with just nine.
Barcelona retained a one-point lead over Real on Saturday when Pedro netted twice and Thierry Henry scored his first of the season in a 4-2 home win over Real Mallorca.
Real went 3-0 up at struggling city rivals Atletico and just managed to hold on for a 3-2 victory despite having Sergio Ramos sent off midway through the second half.
COOL FINISH
Brazil striker Luis Fabiano gave Sevilla the lead at the Sanchez Pizjuan with the first of his two goals after eight minutes before Robert Pires combined with Bruno Soriano to equalise for Villarreal just before the half hour.
The 36-year-old French midfielder ran on to Bruno's chipped return ball and volleyed superbly past Andres Palop.
David Fuster rifled home to give Villarreal the lead just before the hour mark but it was cancelled out by Fabiano two minutes later when he headed his second. Kanoute came on for Alvaro Negredo after 62 minutes to give Sevilla the points.
In Valencia, Villa's Spain team mates Juan Mata and David Silva combined to put the home side ahead after 17 minutes at the Mestalla when Silva's pass sent Mata clear and he finished coolly past Javier Lopez Vallejo.
Villa doubled the lead five minutes before the break, tapping home a Pablo Hernandez centre, and returned the favour by crossing for Hernandez to score a third two minutes later.
Zaragoza's Colombian midfielder Abel Aguilar grabbed a consolation for the mid-table side with 25 minutes remaining.
In Sunday's earlier matches, Athletic Bilbao won 2-0 at Racing Santander and Sporting Gijon beat visiting Espanyol 1-0 thanks to a third-minute goal from Croatia striker Mate Bilic.
Osasuna, who held Barca to a 1-1 draw last weekend, lost 2-0 at Hugo Sanchez's Almeria and Xerez climbed back off the bottom above Malaga with a 0-0 draw at Real Valladolid.
Xerez have only scored three goals in 10 games in their first season in the top flight and conceded 16.
