US Open champion Andy Murray, the title holder in Tokyo, enjoyed a day off from the singles to team up with brother Jamie in a successful start to the defence of their doubles crown.
Czech Berdych, who won the Japan Open in 2008, blasted nine aces as he strolled to his 50th win of the year.
"I served well and took my chances," the second seed said after moving another step closer to qualifying for the season-ending World Tour Finals.
"I'm not there yet," added the world number six, referring to next month's eight-man London shootout.
"I need to keep playing well and stick to my tennis. Not talk about it but bring my best game and that's the best way to qualify."
Berdych, who upset Roger Federer on his way to last month's U.S. Open semi-finals, will play Japan's Kei Nishikori in the last eight of the $1.2 million hardcourt event.
Eighth seed Nishikori hit back in style after dropping the first set to record a 5-7 6-1 6-0 victory over Spain's Tommy Robredo.
Third seed Janko Tipsarevic also progressed with a 6-4 6-2 victory over Swiss qualifier Marco Chiudinelli.
The Serb faces sixth seed Milos Raonic next after Tipsarevic's compatriot Viktor Troicki retired against the Canadian because of a calf injury at 3-0 down in the first set.
Raonic had warmed up for the match with a rickshaw ride around Tokyo's sacred Asakusa district where he also spent time looking at a collection of samurai swords.
Marcos Baghdatis of Cyprus battled past fourth-seeded Argentine Juan Monaco, last year's Kuala Lumpur winner, 7-5 1-6 6-3. He will now face Russian qualifier Dmitry Tursunov who downed local favourite Tatsuma Ito 7-5 6-3.
London Olympic gold medallist Andy Murray takes on Switzerland's Stanislas Wawrinka in the quarter-finals on Friday.