Motherwell's hopes of reaching the Europa League group stage for the first time in their history are over for another season.
Trailing 2-0 following last week's first leg at Fir Park, Stuart McCall's men were unable to turn the tie around at Ciutat de Valencia and were eventually beaten 3-0 on aggregate.
After doing well to hold their opponents to a scoreless opening 45 minutes, the SPL side tired in the second half.
Nabil El Zhar went close to opening scoring with a superb solo effort, but it was Theofanis Gekas who made the breakthrough, finishing off a low cross from Juanlu with an expertly-taken half-volley 18 minutes from time.
Levante are now unbeaten in their last four matches at home.