Michel Bastos scored from the spot early on and he doubled the lead with a deflected drive. Hapoel set up a nervy finale when keeper Vincent Enyeama wrong-footed opposite number Hugo Lloris from the spot, but Miralem Pjanic pounced to seal the points for Lyon.
Schalke got their campaign up and running with a 2-0 home victory over Portuguese giants Benfica, a win that sends the Germans up to second in the group.
Jefferson Farfan fired home the opener with only 17 minutes remaining at the Veltins Arena, before Klaas-Jan Huntelaar collected a Jermaine Jones pass to wrap it up.
The all-important goal came in the 17th minute when Steven Naismith flicked home from inside the box after Kirk Broadfoot headed on Steven Whittaker's pass.
Barcelona had to come from behind to earn a point in their second Group D match at Russian side Rubin Kazan.
Noboa celebrates putting Rubin ahead from the spot
The hosts went in front on the half-hour mark when Cristian Noboa slotted in from the spot, only for Barca - for whom Lionel Messi returned from injury - to level with a penalty of their own courtesy of David Villa.
Danish side FC Copenhagan took advantage to storm to the top of the group after a second surprise victory, this time 2-0 at Greeks Panathinaikos in Athens.
Dame N'Doye - against his former club - and Martin Vingaard struck in the first half, with the home team having ex-Arsenal midfielder Gilberto Silva sent off after the break.
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