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.
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.
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.
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.
