Continuous rain in the sessions shook the field up somewhat, but it was not enough to derail Mercedes' dominance, with Hamilton qualifying over half a second clear of Red Bull's Daniel Ricciardo in second.
The Australian out-qualified his world champion team-mate Sebastian Vettel for the third time this season. The German starts third ahead of Mercedes' Nico Rosberg who will count the cost of a spin at the last turn on his final flying lap.
A miserable week for Ferrari was compounded by Kimi Raikkonen's failure to reach the top-10 shootout, placing 11th, although Fernando Alonso will start Sunday's race in fifth.
Alonso's positive placing is tempered somewhat by the fact he qualified 1.777 seconds off the pace of former McLaren colleague Hamilton.
Saturday's qualifying belonged to the Brit though as he topped the timesheets in all three sessions, despite slippery conditions at the Shanghai International Circuit.
Ricciardo had gone quickest in a damp final free practice session earlier in the day, but any information gleaned quickly became useless as the heavens opened.
Sauber's Esteban Gutierrez joined the usual suspects at Caterham and Marussia in dropping out of Q1, Pastor Maldonado will be last on the grid if he manages to fix an oil leak that prevented him from running for Lotus.
There was better news for Lotus' other driver, however, as Romain Grosjean shook off his team's woes this season to get into Q3 for the first time, settling for 10th place.
Raikkonen's surprise elimination from Q2 helped the Frenchman get through, with McLaren pair Jenson Button and Kevin Magnussen also surprisingly dropping out.
Toro Rosso's Jean-Eric Vergne also made Q3 for the first time this season, qualifying ninth behind the Force India of Nico Hulkenberg, with Williams duo Valtteri Bottas and Felipe Massa ahead of the German.