Stuart McCall's men went to Greece knowing that two goals in normal time would take them to extra-time and started off the brighter but were put to the sword
The Scottish Premier League side were already losing 2-0 from the match at Fir Park and fell further behind on the 50th minute as Lazaros Christodoulopoulos hit a free kick before Charias Mavrias and Ibrahim Sissoko sealed the victory.
The away side needed two goals to take the game into extra-time and they started off the strongest. James Murphy was holding the ball up well as Motherwell were enjoying some of the early possession.
It took until the 27th minute before either side had a proper chance and it came on the back of all the Scottish outfit’s dominance.
Keith Lasley decided he would take matters into his own hands and rifled in a shot from almost 20 yards but it was saved well.
Shots were coming thick and fast and the Panathinkaikos defence had to stand firm as Nicky Law and Omar Daley shot from range as Stuart McCall's side desperately tried to claw back the deficit.
Lasley once more tried from distance but this time his effort rose over the bar just before the break as the two sides went in level on the night.
The 50th minute saw the first goal of the game and it came against the run-of-play. Christodoulopoulos - scorer in the first-leg - floats are delightful free kick over the wall and into the back of the net – breaking Motherwell fans’ hearts in the process.
Moments later, Panathinaikos had a strong shout for a penalty when the ball hit Ramsden’s arm but the referee waved away appeals, then just shortly after Randolph palmed away Toche’s point blank header.
The tide of the game changed with the goal and Jean-Alain Boumsong flicked his header over the bar from another Christodoupoulos free kick.
It was finally game over with under 15 minutes remaining and it was impact substitute Mavrias again. After scoring with his first touch last week, he did it again. He swept the ball past Randolph as Motherwell’s defence fell apart.
The Greek's added gloss on an easy second-half victory when Sissoko chipped over the onrushing goalkeeper to make it 5-0 on aggregate.