Alexandre Lacazette struck an equaliser three minutes from time to deny Hapoel Tel Aviv a place in the Europa League but it was not enough to give his Lyon side top spot in Champions League Group B.
After an entertaining but goalless first half Lisandro Lopez and Ben Sahar traded goals within a minute of each other around the hour mark before Eran Zahavi made it 2-1 to the visitors.
That would have been enough for third place and a parachute into the last 32 of the Europa League, but Lacazette popped up late on for a Lyon side who finished second to Schalke.
Lopez had the first chance of the match, getting away a right-footed shot after five minutes but missing the target from 20 yards.
Bafetimbi Gomis was next to try his luck for the hosts in the 20th minute but his left-footed effort was also off target.
The Israelis were forced into a change up front soon after when Itay Shechter went off injured to be replaced by Sahar.
The pace picked up a little as the game progressed, with Vincent Enyeama pulling off a smart save from Miralem Pjanic in the 27th minute only for Hapoel to go straight down the other end of the pitch and almost score themselves.
Toto Tamuz was the man to try his luck from the edge of the penalty area and was only denied by Hugo Lloris' wonderful save.
Both sides had new chances within seconds, Jean Makoun and Zahavi failing to convert before Jimmy Briand smashed a shot at the Hapoel goal where Enyeama was again on hand to defend his line.
The Ligue 1 side started to dominate proceedings now, Maxime Gonalons and Pjanic both going close from long-range before Gomis hit another fine attempt from 30 yards, where the busy Enyeama again saved to keep the match goalless at half-time.
Enyeama looked like being the difference between the sides when he produced another fine save from Makoun two minutes after the restart, though Lloris matched him with a point-blank block from Gil Vermouth.
Lopez eventually defeated the Nigerian goalkeeper after an hour's play when he picked up possession inside the Hapoel half before driving in left footed from 12 yards.
Sahar responded from an almost identical position virtually direct from kick-off, with less than a minute passing between goals.
The equaliser emboldened Hapoel, with Sahar twice going close before Zahavi brilliantly converted Salim Toama's cross to make it 2-1 after 68 minutes.
Lacazette earned Lyon a deserved equaliser 20 minutes later, slotting home from 12 yards to deny Hapoel the points that would have put them into the Europa League draw.