The Yellow Submarine had enjoyed a decade of unprecedented highs following their team before the club's shock relegation from the top flight at the end of the 2011/12 season - having finished fourth the previous season.
After winning promotion back to the elite at the first attempt, Villarreal played their first home match back in La Liga - only for it to start badly.
Javi Guerra put the visitors ahead after just four minutes before Giovani Dos Santos equalised with a penalty seven minutes before half-time.
There were few clear-cut chances in the second half and the game appeared to be heading for a draw only for Cani to intervene.
Valladolid made a dream start to the game, going ahead inside the first four minutes.
Zakarya Bergdich sent the ball in from the right which found Javi Guerra and the striker slotted home into the bottom left-hand corner of the goal.
Mario Gaspar had a header comfortably gathered by Diego Marino with the goalkeeper punching Manu Trigueros' corner clear as the hosts attempted a quick response.
Cani then fired over the bar from Trigueros' corner with Trigueros then firing a free-kick towards goal which Marino comfortably held.
The first half was ticking down but the hosts found themselves on level terms from the penalty spot seven minutes before the break.
Gilberto Garcia fouled Jaume Costa and Dos Santos slotted the resulting penalty into the bottom left-hand corner the goal.
There were few clear-cut openings at the start of the second half.
Cani's 25-yard shot was comfortably saved by Marino while Trigueros' corner caused a few flutters in the Valladolid box before it was finally cleared.
Jesus Rueda had a long-range shot blocked for Villarreal who had shown nothing as an attacking force really since their goal.
Cani reciprocated although Marino had no problems dealing with his 20-yard effort and it was hard to see where any breakthrough may come from.
Vueda headed wide before Villarreal took the lead with six minutes to go.
Jeremy Perbet's cross from the left wing found Cani and he fired the ball home into the top right-hand corner of the goal.
Valladolid attempted a quick response, Julian Omar Ramos' shot from the rigth punched clear by Andres Sergio Asenjo.
Perbet's shot was cloecked by Marino as the hosts ended on top.