Fryatt bagged the first from the penalty spot and then headed home a second to spark celebrations from the 2,141 travelling fans.
Southend created the better chances either side of half-time, but it was Leicester who broke the deadlock in the 60th minute when referee Clive Penton awarded a penalty for handball against Simon Francis.
Fryatt confidently fired his spot-kick low to the right, with Southend goalkeeper Steve Mildenhall diving the opposite direction, although Fryatt was booked for over-celebrating his 30th goal of the season.
And Fryatt ensured City took the title in the 69th minute when Lloyd Dyer's curling free-kick from the right bounced back off the crossbar and the striker headed home from close range.
The Shrimpers' best opportunities came through Theo Robinson's 20-yard effort which a diving David Stockwell turned around the post in the first half, before blasting the ball against the crossbar after the break.