Jonas scored from the penalty spot as Valencia won 1-0 away to Lille in the Champions League on Wednesday, although it was not enough to guarantee top spot in Group F because Bayern Munich also won.
Bayern, which thrashed BATE Borisov 4-1, finished top of the group because of a superior head-to-head record with Valencia - beating the Spanish club at home and drawing away.
Lille finished in last place behind Belarusian club BATE and failed to qualify for the knockout stage for the second straight season.
Jonas, who scored both goals when Valencia beat Lille 2-0 at home in October, scored from the spot in the 36th minute after being fouled by Lille defender Marko Basa.
The French club went close to equalizing late on.
Lille pushed forward in numbers in the closing stages, forcing four corners in two minutes, and Valenica goalkeeper Vicente Guaita made a tremendous save in the 84th, tipping Salomon Kalou's close-range effort around the post after he expertly brought down a long ball.
Finally showing the attacking intent it should have done at the start of the campaign, Lille almost scored again two minutes later when winger Dimitri Payet's curling free kick hit the crossbar. Striker Nolan Roux headed wide in the last minute from a good position, and Basa went close in injury time with a bicycle kick.
Guaita made another good save early in the second half to deny striker Gianni Bruno, but up until then Valencia had been the better side as Lille looked short on ideas and lacked creativity.
Midfielder Sofiane Feghouli was a threat for Valencia early on with his darting runs down the right, and he had a great chance to play in midfielder Ricardo Costa, only to over-hit the pass.
Returning to play against the club which sold him to Valencia last season, France center half Adil Rami rose to meet a free kick in the 18th but Lille goalie Steeve Elana made a smart save.