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.
Benfica qualify for the last 32 of the Europa League.
Lyon started well but had a goal disallowed when Bafetimbi Gomis was flagged offside as he headed home in the 13th minute.
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.
POOR DEFENDING
Toto Tamuz and substitute Sahar then combined well in the area, making the most of some poor defending by Cris and Papa Diakhate, only for Lloris to pull off a fine save.
Hapoel goalkeeper Vincent Enyeama was also made to work hard in a scrappy but entertaining contest.
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.
The visitors were quick to respond.
Sahar, who had come on for the injured Shechter in the first half, collected a defence-splitting pass from Shay Abutbul and fired past Lloris to equalise.
Six minutes later, Zahavi made it 2-1 to the visitors when he was left alone in the area by the sleeping Lyon centre backs and beat Lloris with a brilliant overhead-kick.
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.
