Rene Girard's men came into the Ligue 1 clash knowing a win would see them seal third spot and a place in the qualifying round for Europe's premier club competition.
All looked to be going to plan when Salomon Kalou put them ahead in the 32nd minute, but Wahbi Khazri's late header forced them to settle for a point.
It could have been worse for the visitors but Bastia substitute Florian Raspentino had a goal controversially ruled out for offside in the final few minutes.
The result leaves Lille eight points clear of Saint-Etienne, who host Montpellier on Sunday, when only a victory will keep them in the hunt for a top-three finish.
The visitors made a strong start, Nolan Roux wasting the first real chance of the game in the 17th minute when he sent a tame effort straight at Mickael Landreau.
Roux was on target again five minutes later, but once more Landreau was able to comfortably hold his header from eight yards.
Bastia's Gianni Bruno twice saw goalbound efforts blocked inside the area in quick succession, and Lille immediately broke away to move in front.
Kalou spearheaded the counter-attack, picking up Roux's pass before cutting in from the left and planting a precise finish into the far corner.
The Ivorian ought to have doubled his tally 10 minutes after the interval, but somehow failed to turn the ball home from three yards out after Simon Kjaer's front-post flick-on.
Lille were made to pay for that miss five minutes from time as Khazri rose highest to meet Raspentino's cross, glancing a fine header into the top corner.
The hosts thought they had stolen it a minute later as Djibril Cisse, on as a replacement for Bruno, saw his shot turned in on the line by Raspentino, but the linesman's flag was raised and Bastia's protests fell on deaf ears.
