The Spaniard headed the Blues into the lead four minutes before the break – his third league goal in four games – before N’Golo Kante doubled Chelsea’s advantage at his former stomping ground with a low shot in the 50th minute.
Thibaut Courtois’ foul on Jamie Vardy in the area handed Leicester a lifeline, with the striker converting his resulting spot-kick, but the Premier League champions held on for the win.
Much of the pre-match talk surrounded the return of Eden Hazard from an ankle injury and Danny Drinkwater who completed a deadline-day move from Leicester to the champions.
Despite Hazard impressing for Belgium with his two substitute appearances against Greece and Gibraltar during the international break, the winger was left on the bench along with Drinkwater.
Instead, Conte opted to start Cesc Fabregas – who scored in the 2-0 win over Everton – and Pedro alongside Morata as Willian was also left out of the line-up for the visitors.
But after a lively start which included Vardy driving Riyad Mahrez’s through-ball wide of the far post, the Blues found the opener through their new striker Morata.
The Spaniard, who joined Chelsea from Real Madrid this summer, put the visitors in front in the 41st minute after superbly heading Cesar Azpilicueta’s cross from the right past Kasper Schmeichel.
It was a carbon copy of Chelsea’s second goal against Everton before the international break, which handed Conte’s side the confidence they needed to go on and score their second of the afternoon shortly after the break.
The goal came from Kante, who had earlier received a warm reception from the Leicester fans, after he latched onto the ball in midfield and then succumbed to the chants of ‘shoot!’ from the travelling fans.
The France international appeared to surprise everyone with his resulting, and seemingly speculative, effort which hurtled along the pitch past several players and into the bottom corner.
But if Chelsea thought the three points were already secured with Kante’s low strike then the champions were handed a major scare when a penalty was awarded for Courtois’ foul on Vardy in the area.
(Chelsea FC via Getty Images)
In his attempt to clear the ball, the Chelsea goalkeeper caught Vardy, who then went on to make no mistake from the spot as the striker smashed a powerful effort past Courtois in the 62nd minute.
Conte reacted to the scoreline by bringing on Willian, new signing Davide Zappacosta and finally Hazard – who hadn’t played for Chelsea this season due to ankle surgery earlier in the summer.
And Hazard and Zappacosta immediately combined to nearly produce a goal when the Belgian’s pass found the Italian, whose low effort flew wide of the post.
Morata was then left incensed when his header hit Harry Maguire’s outstretched arm in the box but saw no penalty given, but Chelsea held on to secure the three points.