Substitute Alexandre Lacazette saved Lyon, who had already qualified for the knockout stage, denying Hapoel a Europa League spot in a lively game at the Gerland stadium.
Lyon took the lead just past the hour through Lisandro Lopez but the visitors were level a minute later thanks to Ben Sahar and went ahead through Eran Zahavi's superb bicycle-kick.
Lacazette's goal left the French side on 10 points in second place behind Schalke 04, with 13 after their 2-1 win at Benfica who came third with six points ahead of Hapoel on five.
Hapoel also looked dangerous, especially on the break, and repeatedly threatened Hugo Lloris's goal as the Lyon defence struggled to keep the opposing strikers at bay.
Etay Shechter and Douglas da Silva found themselves unmarked in front of goal but neither managed to connect with Gil Vermouth's cross.
The Nigerian produced a brilliant save to deny Miralem Pjanic in the 28th and two minutes later parried Gomis's long-range attempt.
He was beaten by a Cris header from Pjanic's corner but Gil Vermouth cleared the ball off the line.
Lyon were rewarded in the 62nd minute when Lisandro slotted home after Enyeama failed to properly clear Jimmy Briand's shot.
Lyon piled the pressure on and Enyeama made a couple of stunning saves to deny Lisandro but there was nothing he could do to block Lacazette's powerful strike from Lisandro's cross.
