Looking to bounce back from successive Ligue 1 defeats, Lyon made a perfect start against RotBlau, opening the scoring with just three minutes on the clock.
The goal was largely self-inflicted by the visitors, who gave away possession when the experienced Marwin Hitz played a lax pass that was cut out by an alert Mathys De Carvalho, allowing Corentin Tolisso to delicately lift his finish past the onrushing goalkeeper.
Albian Ajeti soon saw his close-range effort blocked after Xherdan Shaqiri had been denied a shot at goal moments earlier, but that proved to be a rare attack of promise as Basel struggled to muster a first-half response.
Lyon certainly had chances to double their advantage before the break, with Martin Satriano arrowing a strike across the face of goal when a pass was on.
Involved again as half-time approached, the Uruguayan saw a tame header well held, leaving his side with a slender lead at the break.
Having now scored in 12 consecutive games across all competitions, Les Gones were very much in control of the contest, and they could have turned that dominance into a second goal were it not for a sharp save from Hitz, thwarting Malick Fofana at his near post after the restart.
Basel were being restricted to half-chances, though they did force crucial interventions from Tyler Morton, who cut out a menacing Philip Otele delivery, and Clinton Mata, who swiftly mopped up when Ajeti was bearing down on goal.
Buoyed by a fervent home crowd, Lyon kept the visitors at bay, with Dominik Greif making an important save to deny Leo Leroy a golden opportunity to equalise as time ticked away.
Ultimately, Afonso Moreira's 90-minute strike got the French side over the line, ending Basel’s run of three straight wins in all competitions without conceding.
As for Lyon, it’s now just one defeat in 18 Europa League group stage/league phase outings at the Groupama Stadium (W14, D4), highlighting their pedigree at this level as Paulo Fonseca’s side sit comfortably inside the top eight spots after three matchdays.
Flashscore Man of the Match: Corentin Tolisso (Lyon)