Jonas' scored deep into injury time to ensure Valencia will finish in third for the third successive season, deepening Villarreal's relegation fears in the process with a narrow 1-0 win.
A wonderful goalkeeping performance from Diego Lopez looked to have snatched a point for the visitors as he denied twice denied Pablo Piatti and Aritz Aduriz, before Pablo Hernandez also hit the post late on.
However, two minutes into stoppage time, Jonas controlled Aduriz's flick-on and smashed the ball past Lopez to win the game in dramatic fashion.
Villarreal are now just a point above the drop zone and need to beat Atletico Madrid on the final day to guarantee their 12-year stay in the Primera Division does not come to an end next weekend.
Piatti was first to threaten for the hosts as his drive was well held by Lopez, before Bruno forced Vicente Guaita into his only serious save of the entire game eight minutes later with a powerful drive from the edge of the area.
Valencia's dominance produced far more chances after the break, though, as Aduriz volleyed straight at Lopez four minutes into the second period, before Piatti missed a golden chance to give the hosts the lead as he fired off target when clean through on goal moments later.
Borja Valero and Jordi Alba then saw shots fly just wide at either end, before Lopez returned to centre stage as he somehow got down to turn Aduriz's header away from close range.
Substitute Hernandez then came within inches of finally breaking the deadlock as he nipped in ahead of Lopez but saw his effort come back off the upright.
However, just when Villarreal seemed they could hold out for a vital point, Aduriz headed into Jonas' path and the Brazilian showed great control to bring the ball down before lashing in his third goal in two games to guarantee Los Che's direct entry into next season's Champions League group stages.
