Both drivers made strong starts from the front row and defended perfectly from the hard-charging Max Verstappen to maintain position on the downhill turn to Turn 1.
Valtteri was first to stop for fresh tyres, pitting on Lap 23 and switching from the Soft to the Medium compound, with Lewis following suit one lap later.
Lewis went on to dominate the race, taking his 71st career victory - his 50th with Mercedes-AMG Petronas Motorsport, ninth of the 2018 season and fourth at the Suzuka International Racing Circuit.
Valtteri drove a superbly managed race to clinch P2 and complete the second 1-2 for the team in as many races with his first podium at the Japanese Grand Prix and 30th podium finish in Formula One.
Today's result marks the fifth consecutive win in Suzuka for Mercedes-AMG Petronas Motorsport and a tenth win at the Japanese Grand Prix for Mercedes-Benz Power.
Lewis (331 points) now leads the Drivers' Championship by 67 points from Sebastian Vettel (264 points) with Valtteri (207 points) in P3 and a maximum of 100 points left to be scored in the season.
Mercedes-AMG Petronas Motorsport (538 points) lead Ferrari (460 points) by 78 points in the Constructors' Championship with 172 points remaining to be scored.
Matt Deane, Chief Mechanic, accepted the Constructors' trophy on behalf of the team up on the podium in front of an incredible crowd who have been incredible all weekend!