The hosts wasted a great opportunity to put one foot in the group stages just a few moments later when Antoine Griezmann found himself clear on goal but chipped his effort straight into the hands of Anthony Lopes.
Sociedad were sure they would be gifted with another chance to take the lead late in the first half when Carlos Vela looked to be fouled inside the area but the referee disagreed and harshly booked the forward for diving.
The Spaniards started the second half brightly and were inches away from taking the lead on the night when Haris Seferovic cut inside and rattled the post with a powerful low drive.
However, the Sociedad supporters were not made to wait for too much longer as Vela took advantage of some poor marking in the 67th minute to head home Griezmann's cross from close range.
Lyon's challenge diminished following the goal and Sociedad were able to add some gloss to the scoreline in stoppage time when Vela added his second of the night with a clever chipped finish.