The red-hot world number 30 triumphed in Washington and Cleveland in August and she produced a string of giant-killing upsets in the Japanese capital on the way to another title.
Samsonova beat Wimbledon champion Elena Rybakina and two-time Grand Slam winner Garbine Muguruza and did not drop a set all week.
Fast-rising teenager Zheng was appearing in her first WTA final after knocking out top seed Paula Badosa in the second round.
The 19-year-old went toe to toe with Samsonova in a tight match but had her service broken late in the first set to let the Russian take control.
Both players traded breaks midway through the second set but the decisive moment came when Samsonova took a 6-5 lead to serve for the match.
The 23-year-old calmly picked off her opponent in the final game and sealed the deal when Zheng hit a return wide.
Samsonova's win came after a host of big names made early exits from the tournament.
US Open semi-finalist Caroline Garcia of France joined Badosa in a second-round exit, while Japanese home favourite and defending champion Naomi Osaka withdrew with abdominal pain.
The tournament was being held for the first time since 2019 because of the pandemic.
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