The visitors had offered little as an attacking force before Scott netted an excellent solo goal in the 28th minute and he supplied another impressive finish five minutes later.
The 19-year-old's only other Ladbrokes Premiership goal this season was a spectacular effort against St Mirren and the attacker vindicated his first start since October 19 as he came close to a hat-trick on several occasions.
Allan Campbell netted from close range midway through the second half to continue the trend of Motherwell's academy graduates netting against the Buddies – Campbell, David Turnbull, Jake Hastie and Chris Cadden were all on target against the Paisley side last season.
St Mirren players had been handed an extra incentive after their fans launched an appeal to raise money for Renfrewshire Food Bank, pledging at least £2269 per point gained in their four matches before Christmas. But their team never seriously threatened until stoppage-time as they slipped to the bottom of the table.
The home side were missing Sam Foley with a tight hamstring and they suffered an early blow when Gary MacKenzie pulled up with a similar injury. Cammy MacPherson came on at right-back with Paul McGinn moving inside.
McGinn was not far away with an overhead kick as St Mirren enjoyed the better of the play before Scott conjured up the opener. The teenager, playing wide right, collected Liam Grimshaw's pass down the line, cut inside Calum Waters and kept going before drilling a left-footed strike into the far corner from 20 yards.
Scott doubled the lead after Saints lost possession midway inside their own half. Liam Polworth quickly split the defence and Scott shot high into the net from just inside the box.
The Scotland Under-21 international came close to a seven-minute hat-trick when he headed just wide and he threatened again when his 20-yard effort deflected wide.
Motherwell were missing skipper Peter Hartley but Bevis Mugabi was proving an able deputy in central defence as he got back to foil Jon Obika after the forward looked like he might capitalise on a long ball.
The visitors put the game out of sight in the 67th minute after a slow start to the second half. Saints gifted possession to Jermaine Hylton on the centre spot and the winger jinked his way to the edge of the six-yard box before his fluffed shot fell kindly for Campbell to knock home.
Ryan Flynn soon headed off the line as Motherwell striker Devante Cole tried to force the ball home after a corner.