Lille took the lead twice through Ayase Ueda and Alexsandro, but Real Betis refused to surrender as Marc Bartra scored twice before Troy Parrott completed the turnaround with the winning goal.
The victory gave Manuel Pellegrini's side a dream return to the Champions League after a 21-year absence.
Ueda Gives Lille Early Advantage
Lille made a fast start and were rewarded after just 12 minutes.
Ayase Ueda found the breakthrough to put the French side 1-0 ahead and give Betis an early setback.
The visitors responded positively, however, and gradually began to create opportunities of their own.
Bartra Levels for Betis
Betis eventually found their equaliser in the 33rd minute.
Marc Bartra rose highest inside the Lille penalty area and headed the ball beyond goalkeeper Berke Özer to make it 1-1.
The equaliser briefly shifted the momentum towards the Spanish visitors, but Lille regained their advantage before half-time.
Alexsandro Restores Lille's Lead
Three minutes after Bartra's equaliser, Lille struck again.
Alexsandro headed home in the 36th minute to restore Lille's lead at 2-1.
Lille went into the interval ahead despite Betis showing enough attacking threat to suggest the game was far from settled.
Bartra Strikes Again
Betis returned from the break with renewed purpose and quickly levelled the contest for a second time.
Bartra completed his brace in the 49th minute, heading home again to make it 2-2.
The experienced defender became the central figure in Betis' fightback, scoring twice to erase Lille's two advantages.
Parrott Completes the Comeback
Betis completed the turnaround four minutes later.
Troy Parrott scored in the 53rd minute, producing the decisive finish to put the visitors 3-2 ahead.
The goal capped a dramatic turnaround and continued Parrott's impressive start to life at Betis. The Irish forward had already scored against Real Madrid in La Liga before making his mark on his Champions League debut.
Lille Reduced to 10 Men
Lille's task became even more difficult in the 56th minute when Ethan Mbappé was sent off.
The Lille forward was shown a red card following an incident involving Betis defender Natan, with the decision reviewed by VAR.
Playing with 10 men, Lille were unable to find another equaliser as Betis managed the remainder of the contest.
Betis Complete Memorable European Comeback
The final whistle confirmed a 3-2 victory for Real Betis, despite Lille twice taking the lead.
For Lille, the defeat will be particularly frustrating after twice putting themselves in front and controlling significant periods of the first half.
Betis, meanwhile, showed considerable resilience to overturn the deficit and claim three points on their return to Europe's elite competition.
The result gives Pellegrini's team an excellent start to their Champions League campaign, while Lille will have to regroup quickly ahead of their next European assignment.