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 tonight against a Levante side who beat Real Madrid last season and topped La Liga in late October.
Higdon overcame a knock but the injured Nicky Law, Tom Hateley, Steven Saunders, Simon Ramsden and Shaun Hutchinson, who was sent off in the first leg, were all left at home.
Stuart Carswell came into midfield alongside Steven Hetherington while Fraser Kerr and Adam Cummins kept their places in defence to complete the quartet of under-20s. Jonathan Page replaced Hutchinson at centre-back with seven players aged 23 or under in Stuart McCall's team.
Levante named a strong team with Pape Diop included after the Senegal midfielder missed the first leg after failing to secure a visa to enter the UK.
Having suffered in the heat in Athens on their way to a 5-0 Champions League defeat by Panathinaikos, Motherwell were grateful for a windy night at Estadio Ciudad de Valencia, which was witnessing its first European match.
Motherwell 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 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.
A second Hetherington free-kick two minutes later produced another free header, but Page steered the ball wide from 16 yards.
Levante then forced several corners but the best of the chances saw Gekas and then David Navarro send efforts wide.
Keith Lasley got two shots on target following more Hetherington set-pieces but home goalkeeper Keylor Navas held both, although the second required a sharp movement towards the corner of his goal.
At the other end Jose Barkero fired a powerful long-range strike not far wide and 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.
Stevie Hammell overhit a pass at Page along the back line and the centre-back, after initially chesting the ball down, then underhit his attempted header back to Randolph. Juanlu intercepted but shot wide from 18 yards with only the keeper to beat.
Hammell got the error out of his system 60 seconds later with a forward run and 30-yard shot that zipped just wide and Motherwell were comfortable until the break without troubling the home defence again.
Hetherington was booked 60 seconds after the restart following an aerial challenge and Levante had the first chance of the half when Juanfran's cross found Juanlu, but Randolph got down brilliantly to stop his header, which deflected off 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.
McCall made a double switch midway through the half with Bob McHugh a straight swap for 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.