The race started on a damp circuit in Shanghai, with Hamilton on the pole and Vettel by his side.
Two weeks after beating Hamilton at the season-opening Australian GP, Vettel had to settle for second place this time, finishing 6.2 seconds behind his rival.
When the action got going, Lewis Hamilton led comfortably from the front and was untroubled to pick up another win in China.
Lewis Hamilton powered to victory in the Chinese Grand Prix on Sunday, gaining revenge for his defeat by Sebastian Vettel in the Formula One season opener in Melbourne.
"We are working really hard and trying to close the gap but it's not that easy".
This led to the safety auto coming out on track to ruin Vettel's smart strategic move. Well, anyone driving a Mercedes, a Ferrari or even a Red Bull. The virtual safety vehicle was deplyed on lap 2 after contact between Willams' Lance Stoll and Sergio Perez's Force India and left the former's auto beached on to the gravel.
"Obviously, we were a little unfortunate with the safety auto early on", Vettel said.
Vettel's gamble to change from the Intermediate tire before the two Mercedes wouldn't pay off, however.
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The wet weather conditions would have certainly made the race more interesting between the two but the German driver dropped a few places after deciding to go to the pits just before the safety vehicle was deployed to clear Antonio Giovinazzi's crashed Sauber auto.
That let Hamilton to switch to dry weather tyres without losing position and also allowed both Red Bulls and Vettel's Ferrari team mate Kimi Raikkonen to jump the German.
It was a key victory for Mercedes, which headed into the race second place in the overall standings following an upset victory by Ferrari in Australia last month.
By the time Vettel managed to get past, with a series of spectacular overtaking moves that included banging wheels with his former team-mate, Hamilton was too far ahead.
Meanwhile, Raikkonen was fifth, reporting throttle issues, and only switching to a two-stopper late on.
Bottas finished sixth. The Finn, who has replaced retired champion Nico Rosberg at Mercedes, started third but a spin behind the safety vehicle dropped him down the field.
Fifteen cars finished Sunay's race, with neither McLaren making it to the flag.
Verstappen, who won the Driver of the Day award - voted for by the fans - said he wasn't expecting a top-three finish, given his starting position.