City took a 19th minute lead when Keith Gillespie surged forward and found Danny Tiatto, who set up David Connolly to slot home from seven yards.
Leicester doubled their lead ten minutes later when Gillespie curled in a free-kick which Nyron Nosworthy put through his own goal with a glancing header.
The stadium announcer credited the goal to City defender Matt Heath, but Levein confirmed after the game that the Gillingham defender had made the crucial touch.
After the break Ian Cox came within an inch of adding to the visitors' own goal woes when he headed a Connolly cross against his own crossbar.
Connolly then struck an upright from 18 yards and Lilian Nalis' 20-yard thunderbolt was matched by a magnificent save by Gills keeper Steve Banks.
Gillingham posed little threat - Nicky Southall driving against a post from a tight angle when the Gills were chasing the game, being their only worthwhile effort.
Afterwards Gillingham boss, Stan Ternent said: "We didn't deserve anything from the game. In the first half we were off the pace and in the second half we were left with a mountain to climb.
"Leicester fully deserved their win. I said when I came here there were setbacks along the way and this was one of those days."