Fallon headed the opener after four minutes and struck a second after 41 minutes after Michael Higdon had missed the chance to equalise from the penalty spot in the last-eight contest at Fir Park.
Stuart McCall was at half-time banished to the stand by referee Craig Thomson, the Motherwell manager perhaps still fuming at a perceived injustice which resulted in the corner which led to the opening goal.
Worse was to come for Motherwell, last season's beaten finalists, as captain Keith Lasley was after 69 minutes shown a straight red card for a foul on Fraser Fyvie.
Nicky Law pulled a goal back 11 minutes from time, but the Dons went on to record their first win over the Steelmen in three-and-a-half years to go through to the final four at Hampden.
It was a deserved triumph for the visitors against a team third in the Clydesdale Bank Premier League but below par today.
Well will have the opportunity for swift revenge in Saturday's SPL clash between the teams.
Midfielder Lasley returned from suspension in Motherwell's only change, while Clark Robertson replaced Cup-tied midfielder Gavin Rae in the Dons' only switch following their 1-1 draw with Celtic.
Aberdeen carried confidence from their 12-match unbeaten run into the match and, after Law had an effort blocked, took the lead following a disputed corner. Scott Vernon had appeared to kick the ball out, with Lasley in close attendance.
Fyvie's cross from the right was met at the back post by Andrew Considine, who directed the ball back on to the edge of six-yard box and Fallon headed in his fifth of the season.
The aerial threat of Aberdeen's strike force was soon apparent again when Mitchel Megginson crossed from the right, Fallon headed back to Vernon, who nodded just wide, before Darren Randolph saved well from Rory McArdle.
Henrik Ojamaa was lively for Motherwell, who were awarded a penalty after 27 minutes when Robertson was adjudged to have hauled down Higdon.
Higdon hit his spot-kick at a comfortable height for Jason Brown to save.
Shaun Hutchinson and Ryan Jack each had to be replaced following an aerial collision, Jonathan Page, a substitute after a Stephen Craigan injury in the warm-up, coming on for Motherwell and Chris Clark for the visitors.
Ojamaa prodded wide after the ball broke to him inside the area before the Dons went two up.
Clark's deep cross from the right was met on the left side of the area by Fallon, whose crisp side-footed volley beat Randolph.
McCall was a spectator from the directors' box for the second half and would have been far from satisfied with what he witnessed.
Megginson had an effort saved as the Dons resumed on the attack, with Well far from fluid in possession.
Ojamaa almost created a goal for Law, but Robertson snuffed out the cross from the left and Considine cleared.
Jamie Murphy mis-hit a shot straight at Brown after ghosting in behind McArdle before making way for Chris Humphrey.
Moments later Lasley was sent off for a lunge on Fyvie in the centre circle, with the Dons midfielder taken from the field on a stretcher.
Ten-man Motherwell's hopes improved 11 minutes from time after Humphrey's pace took him clear down the right and he delivered a low cross which Law tucked in at the back post.
Another Humphrey cross failed to find a target in a packed box as Motherwell pushed forward before Kari Arnason's swerving shot was collected at the second attempt by Randolph.
There were five minutes of stoppage time in a frantic finale and defender Tim Clancy was pushed into attack and had a chance to equalise, but Brown saved.
Substitute Peter Pawlett then missed an open goal on the counter attack after Randolph had gone up for a corner, but the Dons still triumphed.