Hamilton, who leads the German in the Formula One standings by 27 points after three wins in four races, lost out for the first time this season and had to settle for second on the starting grid.
The pole on a sunny afternoon in Barcelona was the 16th of Rosberg's F1 career, his first since Abu Dhabi last November, and came as a timely boost in a battle that has seen Hamilton take the upper hand.
"I needed it sooner rather than later," the German told reporters. "It is one step in the right direction to winning the race this weekend. It was a good day in the office."
Hamilton, who had spun in final practice at the exit to turn three, said he had simply lacked the pace.
"Nico did a great job...I don't know if I really have the balance (of the car) where I would like it but I did my best with it and I think tomorrow there is a lot to play for."
Ferrari's Sebastian Vettel will line up in third place with Finland's Valtteri Bottas, in a Williams, alongside on the second row.
The crowd, although sparse in the main grandstands, were cheered by Toro Rosso's Spanish rookie Carlos Sainz taking fifth place on the grid on his home debut.
Hamilton won from pole last year but eight different drivers have triumphed in the past eight years at the Circuit de Catalunya and Rosberg is perfectly placed to continue that trend.
The odds favour the Mercedes duo more than ever in the first race of the European season, with only two drivers having won in Barcelona without starting on the front row.
One of those was home hero and double world champion Fernando Alonso, who will need a miracle to repeat the feat after qualifying 13th for McLaren.
That still represented a step up for the team, with both Alonso and Jenson Button through to the second phase of qualifying for the first time this season, although the problems remained.
"We put new brakes on for qualifying, I don't know what is going on with them but I had really big issues with the car all over the place," said 2009 champion Button.
(Editing by Ed Osmond)
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