Pinnock was given his first taste of first-team football at Aldershot earlier this month, while Nije came off the bench to make his debut in the Carling Cup first-round defeat to Peterborough in August.
Versatile right-sided player Auger is the third youngster to make the step up to Phil Brown's senior squad, much to the delight of Shrimpers' head of youth Ricky Duncan.
Duncan told Echo News: "It's fantastic. Since Phil Brown came in he's been to a number of our games, and that's a big boost for all the players to have the first-team manager watching.
"It's fantastic for everyone involved in the youth set-up that they've been given this chance."