Much of the off-track activity at Suzuka had centred around Hamilton's decision to join Mercedes from the start of next year, with Perez making the switch from Sauber to fill the shoes of the 2008 world champion.
The pair found themselves battling on the track as they ran sixth and seventh in the early going.
Perez dropped behind Hamilton after running wide while trying to pass Felipe Massa, but made a pass on the Briton at the hairpin in a cloud of tyre smoke as he locked up his left-front tyre.
Hamilton regained the advantage after the first-round of pit-stops and, when Perez tried to go around the outside at the hairpin, the Sauber spun off into the gravel and out of the race.
"I saw him coming and I have a championship to fight for and he doesn't, " said Hamilton, who eventually finished fifth and now lies 42 points behind championship leader Fernando Alonso after the Ferrari driver crashed at the first corner.
"I thought that he was going to do a crazy manoeuvre, which he did.
"Then [later] when he was behind me I saw it coming again so I moved a little to the inside, thinking that he was going to go up the inside so he couldn't get by, and he just flew down the outside of me. So very interesting."
But Sauber boss Monisha Kaltenborn said the experience was all part of the learning curve for the 22-year-old.
When asked if Perez had been too keen to prove a point given whom he was racing against, she said: "I don't think so.
"He is a very emotional character, we know that, and he does not have so much experience, so with someone with his character these things happen. It's part of the package you have with a young driver and you have to live with it."