The Brazilian opened the scoring just as the French side seemed most in control of the Group F clash on 38 minutes as he swept home Roberto Soldado's deflected pass.
And the three points were assured for the hosts when Jonas' 74th-minute cross deceived Lille goalkeeper Mickael Landreau to drift in at the back post before the visitors were reduced to 10 men when Mathieu Debuchy was dismissed late on for a second booking.
Both sides were in need of the points after defeats on matchday one and it was Valencia who were first to threaten as a fine through-ball by the returning Fernando Gago put Sofiane Feghouli in on goal but the French-born Algerian pulled his shot miserably wide.
The visitors then took a hold of the game for a spell and should have gone in front when Ryan Mendes' determined run freed Florent Balmont inside the box but he too could not hit the target as he fired beyond the far post.
Vicente Guaita then had to be alive to a long-range effort by Dimitri Payet, but just as Lille were growing in confidence Valencia took the lead as Soldado waited patiently before slipping a ball into the path of Jonas who finished with ease into the bottom corner.
Rudi Garcia's men should still have went in at the break level though as a long ball over the top of the Valencia defence found Payet in acres of room, but he could only smash his effort into the side-netting and with that Lille's last clear chance of an equaliser was gone.
Valencia controlled the game with far more authority in the second half and Spain striker Soldado should have doubled their lead earlier as he headed over with the goal at his mercy from Feghouli's cross.
However, any nerves around the Mestalla were settled 15 minutes from time when Landreau flapped at Jonas' cross and the ball ended up in the back of the net.
And Lille's disappointing evening was rounded off when Debuchy received a second booking for a late challenge on Andres Guardado with four minutes remaining.