The Aberdeen side showed just one change from the team which started at Hamilton last week, Kai Watson coming into central defence to replace the suspended Finlay Murray.
The home team got off to the worst possible start, conceding in the opening ninety seconds of the game. Jamie Shingler made a good save from Spiers at the expense of a corner. After the flag kick was headed behind for a second corner, Bailey Rice fired in a vicious inswinger with his left foot, the ball evading everyone and landing in the back of the net.
Motherwell came close again when Miller saw a shot deflected wide then Adam dragged his shot after a fine run had taken him clear of the Dons rearguard.
The Dons first meaningful attack came on the quarter hour, Bavidge's header from Harvey's cross well saved by keeper Connolly. Five minutes later it should have been level pegging, but Harvey fired wide after an initial Bavidge shot had been charged down.
Six minutes from the break and another chance was passed up, Harvey not connecting properly with his shot after Marshall's lay off allowing Connolly to save.
And this proved costly for the Dons as Motherwell won a spot kick after Fatona downed Spiers in the box, Miller making an immaculate job of the penalty, sending Shingler the wrong way to double the For Park side's advantage.
Two minutes later it was 3-0, full back Wilson being allowed to run twenty yards unchallenged before firing a fine shot past Shingler from the edge of the box.
A poor start and a poor end to the half from the Dons who had given themselves a mountain to climb if they were to get anything from the game.
Half time - Aberdeen 0 Motherwell 3
Aberdeen made a double change at the interval, Oluyemi and Stewart replacing Shingler and Fatona.
Two minutes after the break, Bavidge cut in from the left but saw his parting effort well saved by Connolly. The striker then showed all his pace and power to race down the left and set up Harvey with a neat cutback, but the striker fluffed his lines and the danger was cleared.
Motherwell came more into the game and Hunter was close after a neat turn in the box, then substitute Ferrie forced a solid stop from Oluyemi.
Liam Harvey thought he had reduced the leeway on 70 minutes, but his joy was cut short by an offside flag. There was no lack of effort from the young Aberdeen side against their bigger, more physical opponents. Both sides were very competitive and there were plenty of meaty challenges in the game which saw just the single booking, that of Marshall following a foul on the impressive Miller.
Blessing Oluyemi made another couple of good stops to prevent Motherwell going further clear, but the Steelmen were worthy victors courtesy of their first half goals although the Dons will again rue missing chances which could and should have made the game much closer.
Full time - Aberdeen 0 Motherwell 3
Barry Robson: "It is a common theme. We have struggled massively defensively this year. You see that again tonight with the three goals. They are learning the hard way. We are there to help them as much as they can, but they need to help themselves.
"Also frustrating at the other end with the chances that we missed tonight.
"We are probably the youngest group in the league.
"We are still very young and there was a size difference tonight, their physicality was difficult to deal with when we try and play the way we want to. Credit to Motherwell, they have a strong side. They play percentage football, they play men's football. Our players will get quicker, they will get stronger, they will get better. We will keep working with them until the summer and then you will see a different team next season."