The Foxes made it five wins from six games this summer as manager Brendan Rodgers handed a maiden Filbert Way start to Ayoze Pérez.
A closely-fought opening period yielded few goalscoring opportunities, with Jonny Evans going closest for the hosts, while Josip Iličić and Robin Gosens both had wayward efforts.
Evans headed off target for a second time in the game with 37 minutes on the clock, before City’s best chance of the first half fell to Jamie Vardy, who was denied by Pierluigi Gollini in a one-on-one situation.
After the interval, both outfits traded blows. Pérez first fired over from a tight angle, while Mario Pašalić saw his strike blocked by Atalanta team-mate Luis Muriel.
A superb pass from Belgium international Youri Tielemans then released Pérez for another opportunity, only for the Spaniard to see his strike saved by Gollini.
Pérez persisted, though, and after a fine solo run, he beat two Atalanta defenders before slotting into the bottom corner with 61 minutes gone to score his second goal of pre-season.
City went in search for a second strike, as James Maddison first fired off target before Ricardo Pereira had a long-range shot blocked on the edge of the box.
With 75 minutes to go, after continuous pressure on the Atalanta back line, substitute Christian Fuchs’ instinctive long throw released Vardy, who took a touch to set himself before applying a cool finish into the right-hand corner.
Fuchs had a goal of his own disallowed with six minutes to play, as the former Austria international slammed home, only for his strike to be ruled out as Evans was flagged offside.
The Italian outfit halved the deficit with three minutes to play when Muriel converted a penalty after being brought down by Ricardo, but City’s structured defending saw them see out the win.
Major moment
An even first period on Filbert Way was just about edged by City, who had the best opportunity of the opening 45 minutes when Jamie Vardy was denied by the legs of Pierluigi Gollini.
However, the Foxes impressed after the interval and it was Ayoze Pérez, on his King Power Stadium debut, who struck the opener to set Brendan Rodgers’ men on their way to another victory this summer.
Who impressed?
Speaking to LCFC TV at full-time after commentating on the win, Gerry Taggart said: "I want to give it to Jonny Evans because his first-half performance was excellent, but the finish from Ayoze Pérez was exquisite.
"That obviously set Leicester on their way to winning this game of football. It took a little bit of class to slot that ball home, so Ayoze Pérez just about pinches the Man of the Match award for me."
Coming up…
After a successful and productive pre-season schedule, Leicester City’s sixth-straight season in the Premier League begins on Sunday 11 August (2pm BST kick-off), when Wolverhampton Wanderers visit King Power Stadium.