Michael Higdon had a goal disallowed as an injury-hit Motherwell gave as good as they got in the first half, before Greece striker Theofanis Gekas finished off their Europa League hopes as he converted a cross to complete a 3-0 aggregate win and ensure Levante progress to the group stages.
Motherwell had disappointed in the home leg but they restored pride against a Levante side who beat Real Madrid last season and topped La Liga in late October. The visitors had the ball in the net inside three minutes when Higdon escaped his marker and ran round the back of the defence to head home Steven Hetherington's free-kick.
The decision did not look straightforward but the offside flag was raised instantly, although the linesman's intervention took some time to register among many of the boisterous 400-strong Motherwell support.
At the other end Jose Barkero fired a powerful long-range strike not far wide and Gomez Juanlu saw a curling effort just clear the far post with Darren Randolph at full stretch. Motherwell continued to have their fair share of possession but they almost shot themselves in the foot on 32 minutes.
Hetherington was booked 60 seconds after the restart following an aerial challenge and Levante had the first chance of the half when Garcia Juanfran's cross found Juanlu, but Darren Randolph got down brilliantly to stop his header, which deflected off Adam Cummins.
The Irishman made another great stop on the hour mark, blocking from Nabil El Zahr after the Moroccan had run on to Barkero's pass, which took out Hammell and Cummins. Motherwell were finding possession harder to retain but Higdon almost threaded Henrik Ojamaa through on a break, however the Estonian could not quite get round Navarro.
Manager Stuart McCall made a double switch midway through the half with Bob McHugh a straight swap for Henrik Ojamaa and winger Chris Humphrey replacing Carswell on the right flank.
El Zahr soon missed another great chance, shooting over after turning inside Hammell in the box. A goal for Motherwell would have worried the hosts but Levante made their second-half possession count. They worked the ball to Juanlu on the left wing and Gekas got in front of Cummins to steer the cross inside Randolph's near post from six yards.
A fifth teenager, left-back Zaine Francis-Angol, replaced Hammell but the Lanarkshire side rarely forced their way forward in the closing stages.