Stuart McCall's men have it all to do in the second leg as the La Liga grabbed two vital away goals prior to Shaun Hutchinson's sending off for a professional foul
Gomez Juanlu opened the scoring in the first half after being teed up by Christian Lell and former Liverpool man Nabil El Zhar compounded the hosts' misery after the hour mark.
The Spaniards started the brighter at Fir Park, with Euro 2012 star Theofanis Gekas causing the Scots all sorts of problems.
His close range effort on three minutes went barely wide of the post as the visitors looked to try and nick an away goal from the outset.
Jamie Murphy and Chris Humphrey were stand-out performers for Motherwell in the opening exchanges but David Navarro and Keylor Navas dealt with everything thrown at them with aplomb.
The hosts were standing strong too with Adam Cummins clearing a Nikos Karabelas cross as both sides looked to gain an early advantage.
There was no real chance again until the 16th minute. Vicente Iborra shooting straight at Darren Randolph before the ball was lofted down the other end to Tom Hateley but his effort went wide of the goal.
The game opened up a little more on the back of that exchange, Herrero Michel forcing Randolph into making another save, followed by Munoz Pedro Lopez missing the target completely.
Levante made their pressure pay after 42 minutes when Juanlu scored deep inside the penalty area after being played in by Lell and the half-time lead it secured was little more than the visitors deserved.
The second half saw Levante play deeper as Sergio Ballesteros and Navarro cleared Hateley’s free-kicks and crosses like their lives depended on it.
Motherwell got the ball past the duo on 55 minutes but Henrik Ojamaa’s shot was blocked by Pedro Lopez, and when the ball landed at Ojamaa’s feet, he could only shoot high and wide.
Levante went two up after 61 minutes and again got the assist. He played in El Zhar, who rifled into the bottom left-hand corner from inside the penalty area.
The game slowed down after that last effort as Levante looked to hold on to the all-important away goals they had accrued, though Shaun Hutchinson's dismissal for a professional foul with 14 minutes left made life more comfortable for the Spanish side.
Motherwell go into the second leg knowing that they will need to match this scoreline simply to take the tie into extra time.