Sofiane Feghouli's right-footed shot for Valencia was the only notable chance of the opening half-hour, but the effort drifted wide.
Jonas collected a smart through pass from Spain international Roberto Soldado before firing into the bottom corner.
Payet continued to be a threat for Lille, but could not find his radar, sending several efforts off target.
Brazilian forward Jonas doubled his tally with a fine second on 74 minutes, beating Mickael Landreau from a tight angle.
Reported Premier League target Mathieu Debuchy was sent off late on to end Lille's slim hopes of a comeback, leaving the French side pointless after two matches.