The draw left les Merlus in 18th spot, which means they will now head into Ligue 1’s first ever play-off against third-placed Ligue 2 side Troyes for which team will play in the top flight next season.
Without injured Cameroonian top striker Benjamin Moukandjo, Lorient’s attack struggled against the well-drilled defence of the visitors.
Three points would have seen Lorient into 17th place but their nemesis Bordeaux took the lead via Younnouse Sankhare’s seventh minute header.
Waris went close minutes later after skipping past two defenders but his low shot to the right missed the goal by inches as an agonizing evening started for the capacity crowd who turned up to cheer them to victory.
It took a last ditch effort by Vincent le Goff to restore parity in the 69th minute to keep the home team on the verge of escape.
However, a 91st minute goal by Ronny Rodellin against Paris Saint Germain mean that Caen snatched the final automatic safety spot and left les Merlus players and fans inside the Stade Yves Allainmat deflated at the final whistle.
Lorient would face Troyes over two legs to determine which team would play in Ligue 1 next season and which would play in Ligue 2.
The draw also meant that Bordeaux failed to secure a Europa League spot. Nancy and Bastia have been relegated to Ligue 2.