Jonas converted a penalty nine minutes from the interval as Valencia finished on 13 points, level with Bayern Munich but behind the German team because of a worse head-to-head record.
Lille finished bottom with three points, three adrift of Europa League-bound BATE Borisov.
Valencia were without new coach Ernesto Valverde who will effectively take over from the sacked Mauricio Pellegrino on Thursday.
With former match delegate Salvador Gonzalez 'Voro' on the bench on a temporary basis, the troubled La Liga side did not impress but played solidly.
Lille made the best start but it was shortlived.
Lucas Digne made a good job of containing Sofiane Feghouli on Valencia's right flank early on in a game played under a closed roof.
The left fullback was also at ease going forward, sending a fine cross into the box only for Marko Basa to head over the bar.
Basa brought down Jonas in the box 10 minutes before the interval and the Brazilian beat Steve Elana to convert the resulting penalty.
Lille played nice football but definitely lacked stamina and proved to be toothless up front until the hour when Ronny Rodelin's 10-metre volley was blocked on the goal line by striker Nelson Valdez.
Vicente Guaita impressively palmed away Salomon Kalou's powerful 84th-minute strike to secure the win.
Valencia, 12th in the La Liga standings 22 points behind leaders Barcelona following a mediocre start to the season, travel to Osasuna on Saturday.
