Leclerc delighted with strategy in Japan after fourth place finish
Leclerc, who started eighth, completed 27 laps on a set of medium tyres before switching to hards and defending tenaciously to hold off McLaren's Lando Norris.
The Monegasque driver was eventually passed by teammate Carlos Sainz, who finished third behind the Red Bull 1-2 of Max Verstappen and Sergio Perez.
Despite being voted Driver of the Day, Leclerc dropped down to third in the driver's standings with 59 points, four ahead of teammate Sainz.
Verstappen leads the title race on 77 points ahead of his teammate Perez on 64.
"We did an amazing strategy, amazing time management, amazing pace, but it's just not enough when you're starting from eighth," Leclerc told Sky Sports.
"It's not very often in my career that I had to focus on qualifying days because this normally is one of my strengths. But Australia and here, this is where I've been struggling so I'll focus on that.
"But normally when I work on something I get better quite quickly, so I'm confident."
Team boss Frederic Vasseur said Ferrari had done well to bounce back from their disappointing showing in the final practice session and qualifying.
"We had a very strong Sunday with a good strategy and we were able to come back and if we want to do a better weekend, we'll have to improve the Saturdays," Vasseur added.
"We made a good step with the car during the winter, even the last part of last year, but everybody's much more confident in the team, much more calm and we are doing a good job together."
Sainz once again delivered for Ferrari two weeks after his win at the Australian Grand Prix, claiming his third podium finish in as many races this season.
The Spaniard, who missed the Saudi Arabian Grand Prix while recovering from appendix surgery, is set to lose his race seat to seven-times world champion Lewis Hamilton in 2025.
"Unfortunately, I have no clue where I'm going to be next year. It is true that we're talking to many teams," Sainz said.
"I just need to go keep focused on what I'm doing just prove to myself to everyone that when I'm given a fast car you know I'm maximising what I'm given.
"I deliver you know, it's been a strong start... (Teams) know I'm available. Let's see what happens."