Tosic twice drew solid saves from Bogdan as a second goal seemed inevitable, but Bolton served belated notice of their threat in drawing two superb saves from Reds goalkeeper Amos around the hour mark.
First Tope Obadeyi burst into the United area and only Amos' fingertips prevented the striker's shot from nestling in the bottom corner, but even better was the England youth international's superb reaction to turn Aaron Mooy's free-kick round the post.
Those scares provoked a flurry of United half-chances, as Macheda, Welbeck and Danny Drinkwater all fired narrowly off-target, and only another superb save from Bogdan prevented substitute Magnus Eikrem from putting deserved gloss on the scoreline in the final minute.
One goal was enough, however, and it was fitting that the impressive Tosic should seal a second trophy of the campaign for the Reds' Reserves. Next season will begin with the chance of another - the Lancashire Senior Cup final in August, in which Bolton will again provide the opposition.
United: Amos; Eckersley, C Evans, De Laet, James; Tosic (Stewart, 87), Drinkwater (Eikrem, 87), Possebon, Martin; Welbeck (Gill, 74), Macheda.
Subs not used: Devlin, Dudgeon.