Pinnock and Nije both made their first-team debuts for the club this season, while Auger has been tipped as a star of the future.
Head of youth Ricky 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."
Southend currently sit 11th in the League Two table.