The Ainslie Park side trailed at the interval to Robbie Mason’s header but a second-half double from youngster Atkinson thwarted league leaders Leith’s attempts to win four trophies this season.
The teenager netted his first from the penalty spot in the 65th minute before he conjured up the winner with a great solo effort with just seven minutes remaining.
“He’s done really well for us,” Tomassi said of his frontman. “He’s played in the wide areas for most of the season and scored a lot of goals but we pushed him further forward in the second half up alongside Andy [Howat]. He made the penalty when he got brought down in the box and then put it away before popping up with the winner which is great for the young boy.
“The lads did really well so it was a great win for the club. There was certainly a real determination to win it because I think the boys are a bit disappointed as to where we might end up finishing in the league. Getting the trophy certainly makes up for that.”
Leith, who won the Alex Jack Cup earlier this month, are still overwhelming favourites to win the league title having amassed a 15-point lead over nearest challengers and reigning champions Lothian Thistle Hutchison Vale. Derek Riddel’s men are also still involved in this season’s King Cup.
Lothian Thistle kept up their slim hopes of catching Leith with a 5-2 win away to bottom side Eyemouth United – Scott Gormley, Dean Cummings, Willis Hare, Louis Swanson and an own goal all contributing to a comfortable three points for the Saughton-based club.
Ormiston moved up to eighth as they edged out Craigroyston 3-2 in an entertaining clash at St Mark’s Park while Civil Service Strollers continued their recent run of form with a 4-2 win over Coldstream in the Borders.
Tynecastle are now up to fourth as they thrashed city rivals Heriot-Watt University 6-2 at Saughton Enclosure.