The 19-year-old, currently on loan at Derby County, was picked by Boothroyd after impressing for Frank Lampard's side.
Raivis Jurkovskis opened the scoring for Latvia, before Mount crossed in for Tammy Abraham to head in an equaliser.
Mount scored the winner with just 17 minutes left on the clock. Receiving Abraham's pass, he took the ball on and finished with a low drive into the far corner.
The goal leaves the 'Three Lions' just one point away from qualification.