The teenage striker scored in each half before Jermaine Hylton and Liam Donnelly both notched their second goals of the season.
Scott was supported with an impressive new-look trio behind him.
Sherwin Seedorf and Hylton caused all sorts of problems on the wings after coming off the bench to net in Saturday's 3-0 win over Queen of the South, and Liam Polworth was involved in both of Scott's goals as he filled the void created by David Turnbull's knee surgery.
Former Motherwell striker John Sutton sent a free header wide in the early stages but the hosts soon got a grip of proceedings.
Scott forced a save and then diverted Jake Carrol's strike on to the bar before Seedorf drew a double save from Sam Ramsbottom.
The pair combined to give Motherwell the lead in the 22nd minute after Polworth sent Seedorf clear. The former Wolves player beat a man and the goalkeeper and Scott made sure his shot found the net from close range.
Scott had a good chance to double the lead after another Polworth through ball but he hesitated and the chance was lost.
The visitors came back into it and Aidan Nesbitt had two efforts saved just before the interval but Scott got Motherwell going again with a 30-yard strike which Ramsbottom tipped over.
Seedorf and Hyltyon came close before Scott shot high into the net after Polworth's cutback in the 66th minute.
Hylton made it three with a measured finish from 18 yards six minutes later before Donnelly drilled home in the 82nd minute after Scott's effort was blocked.
Substitute Christian Ilic had a shot cleared off the line as Motherwell continued to threaten.