Rosberg, with a 17-point advantage over Hamilton after winning the opening two rounds of the Formula One season, lapped the circuit in Shanghai in one minute 35.402 seconds.
It left him over half a second quicker than Daniel Ricciardo in his Red Bull after the pole spot bids of the Ferrari duo of Kimi Raikkonen and Sebastian Vettel faltered on their final runs.
Raikkonen, top of the timesheets in the penultimate session of qualifying, had to settle for third fastest after running wide on a corner, with Vettel, who made a similar mistake, in fourth.
It was the first qualifying session since F1 officials decided to abandon the "knock out'" format which was so criticized in Australia and Bahrain by the drivers and fans -- and it was certainly incident-packed.
Britain's Hamilton, a record four-time winner in Shanghai, reported a problem with his power unit before qualifying was halted after Pascal Wehrlein's Manor crashed into a wall.
His Mercedes mechanics battled to sort out the problem, but he did not complete a lap.
Hamilton, who had already been hit with a five-place grid penalty for Sunday's race after a gearbox change, was clearly disappointed by another setback to his bid for a third straight title.
"I'm sure the guys are as gutted as I am," Hamilton told Sky Sports.
"We've got to try stop this happening again."
Rosberg, by contrast, could afford to celebrate his first pole of the season and 23rd overall over race radio.
"Car was great again, sorry that the other car didn't make it," said the German.
After the drama involving Hamilton and Wehrlein, the second session was prematurely halted when the left wheel of Nico Hulkenberg's Force India flew off, leading to a later three-place grid penalty for the German.
Spain's Fernando Alonso, returning to action for McLaren after his horror crash in Australia, was among a number of drivers left frustrated as their bid to make the third and final session was ended without the chance to complete a final lap.
He will start from 12th with teammate Jenson Button one place behind.
Australia's Ricciardo, sporting a new fierce haircut, was the surprise packet of qualifying, while his teammate Daniil Kvyat will start from the third row with Valtteri Bottas in the Williams.
Sunday's race will be the third in a 21-round championship which has been dominated by Mercedes for the past two seasons, Hamilton taking the honors on both occasions from Rosberg.
But his faltering start to the 2016 campaign has raised eyebrows and no driver has won the F1 title in the past four years after failing to win any of the opening three races.