Celta were leading 1-0 at the Madrigal and there were about three minutes left when the canister, which local media said contained tear gas, landed near the visitors' goal and began spewing out a thick cloud of white smoke.
Both sets of players, some of whom were clearly suffering from the effects of the gas, retreated inside the stadium and fans quickly left the ground, with many covering their mouths and noses and in obvious distress.
The game resumed after a half four and Celta's Manuel Agudo scored off a free kick in the 90th minute to give the visitors a 2-0 victory.
Villarreal president Fernando Roig said police are looking for the person who threw the bomb. He said the device had released tear gas and was similar to ones used by police.
"Villarreal condemns and laments what has happened," Roig said. "This type of act in no way represents our fan base, which is calm and controlled. I am convinced that this was done by someone who came from outside to hurt Villarreal."
Celta coach and former Barcelona player Luis Enrique said he had never experienced anything like it in a game before.
"Everyone thought it was a flare, but when we saw (goalkeeper) Yoel (Rodriguez's) eyes, which were bright red, we immediately realized that it was something more dangerous," he said. "This should never have happened."