Orellana had just headed Celta into the lead late in the second half when what appeared to be a smoke bomb was thrown on to the pitch, forcing the referee to take the players from the pitch and leading to most of the supporters leaving the stands.
It led to a lengthy stoppage - and considerable confusion as at one stage it seemed the match would not continue - but eventually the players re-emerged and the four remaining minutes were played, enough time for Nolito to add a second and barely deserved goal for the visitors.
The home side were utterly dominant in the first period but could not find a way through.
Bruno got an early wayward shot away but chances were scarce until Mario volleyed wide midway through the half.
Giovani Dos Santos had two decent chances, a strike from the edge of the box which was held by visiting goalkeeper Yoel and a left-foot shot from inside the area which went wide, while Jeremy Perbet was similarly frustrated.
The game opened up a little after half-time with Celta coming into things more, but it was the hosts who created the half's first opportunity.
Bruno got on the end of a corner from Dos Santos but could not keep his header down.
Santi Mina finally had the visitors' first effort of note four minutes into the second period but his curling effort from 20 yards went wide of the left-hand upright.
Manu Trigueros fired over for Villarreal and Augusto Fernandez went wide left at the other end, before Yoel was again called into action.
The Celta stopper was on hand to parry Bruno's effort in the 55th minute before opposite number Juan Carlos held an effort from Santi Mina just after the hour mark.
Yoel again frustrated the hosts when he blocked a close-range effort from Moi Gomez, then he turned a long-range effort from Tomas Pina behind for a corner.
After 80 minutes Yoel denied Perbet and the goalkeeper was rewarded for his efforts when his side, out of nowhere, took the lead.
The goal came from a set-piece after Gomez fouled Nolito. Alex Lopez sent in the free-kick and Orellana flicked a header home.
Soon after play was halted as a canister thrown from the crown spewed out what appeared to be smoke, with the referee taking the players from the field and fans streaming out of the stadium with many holding their noses and mouths.
Play was halted for nearly half an hour, but when it did eventually get back under way it got worse for Villarreal as Nolito curled home a free-kick from the edge of the box to seal the points for Celta, dealing a serious blow to the Yellow Submarine's hopes of Champions League qualification.