The SPL side were beaten in the Champions League by Panathinaikos and now the experienced La Liga outfit have ended their European ambitions for the season
The Greece striker struck in the 72nd minute to end any hope of the SPL side getting back into the tie after their 2-0 loss in the first leg seven days ago.
That means Stuart McCall’s men will play no further part in European competition this season, having lost to Panathinaikos in their Champions League qualifier earlier in the summer.
Motherwell fared significantly better in the second leg than they had done at Fir Park last week and had numerous first-half chances to revive their chances in the tie.
Michael Higdon thought he had given the visitors a dream start on three minutes but his headed effort was ruled out for offside.
Jonathan Page and Keith Lasley also threatened in the early stages, while Juanlu and Jose Barkero threatened at the other end.
Juanlu should have done much better on the half-hour mark when he capitalised on an error from Stephen Hammell but only fired wide from 18 yards.
After the break, Henrik Ojamaa and Nabil El Zhar exchanged chances and while the Spaniards were exerting more control over proceedings the longer the game went on, the tie was still alive with the score 0-0 on the night.
That was until 18 minutes were left on the clock, when Juanlu found space out wide and whipped in a cross. Gekas got in front of defender Adam Cummins and made no mistake from close-range, sneaking his effort inside the near post.
That ended the tie as a contest but Well continued to battle and almost had an equaliser on the night but Chris Humphrey missed the target with the goal gaping late on.