Arsenal got off to a nervous start and their problems began as early as the fourth minute when Manuel Almunia collided with Giuseppe Rossi. The clash resulted in the Spanish goalkeeper being substituted in the 27th minute with an ankle injury.
First blood went to Villarreal in the tenth minute as Marcos Antonio Senna fired in a sensational shot into the top corner from 30 yards which Almunia has no chance of stopping.
Theo Walcott looked the most dangerous player for the Gunners early on, causing the Villarreal defence problems with his pace, but the longer the game went on the more he faded.
After 30 minutes it could easily have been 2-0 as substitute keeper Lukasz Fabianski managed to pull off a fabulous double save, first from the constantly dangerous Senna and then a from Joan Capdevila's follow-up effort.
Things got worse for the north London club when William Gallas had to be replaced in the 43rd minute after becoming the second Arsenal player to get injured by colliding with former Manchester United player Rossi.
The Spanish club might have been the better side in the first half but things were very different in the second period as the Gunners put Villarreal under plenty of pressure with Cesc Fabregas instigating the majority of attacks.
In the 66th minute the Gunners got that vital away goal with an unbelievable strike from Adebayor. Fabregas' pass into the box was taken on the chest by the Togo striker and he hit an unstoppable volley into the back of the net.
From then on it was one-way traffic as Arsenal put the Spanish side under intense pressure but they were unable to add to their tally. However, they will still be considered firm favourites to progress to the semi-finals.