The German driver is just two points behind Alonso in the 2006 World Drivers Championship, but the Spaniard will have the upper hand on the grid in China with Schumacher starting from 6th position.
Joining Alonso on the front row will be his Renault teammate Italian Giancarlo Fisichella, with the two Hondas behind them on the second row after Brazilian Rubens Barrichello qualified third fastest, and Briton Jenson Button fourth.
Cool weather and rain in Shanghai has seen tyres play a big part in practice and qualifying with Schumacher being the only driver on Bridgestone rubber in the top 10.
"It's very difficult for everybody. We saw a lot of tyre warming on the out laps for everybody and we need to see what happens," said defending champion Alonso.
"I don't know about using the soft tyres - it will be a difficult decision, but we will see."
The Renault and Ferrari teams would both prefer to race on soft-compound tyres provided by Michelin and Bridgestone respectively, but with the possibility of a wet track choosing the correct tyres will be crucial.
"Paradoxically, it may mean we have to use a harder tyre for Sunday than if the temperatures had been higher," said Ferrari technical director Ross Brawn.
"The rubber is operating at a different temperature and it grains more. You get this shearing of the rubber on the surface."
Alonso's pole was Renault's 50th in Formula One and the Spanish driver's 15th - his last start from pole position was in Canada in June where he went on to win the race comfortably.
Ferrari leads Renault by three points in the Constructors Championship with two races remaining after Shanghai, as the Formula One caravan travels to Japan and Brazil to finish the season.