Hamilton hung on despite seeing a 40-second advantage erased with 20 minutes remaining when the safety car emerged after Nico Rosberg of Williams crashed.
Red Bull's Mark Webber was fourth ahead of Sebastian Vettel of Toro Rosso. Rubens Barichello of Honda, Kazuki Nakajima of Williams and Heikki Kovalainen rounded out the places in the points.
The morning rain came and went as drivers took on the tight street circuit without the banned driver aids that help improve traction control.
Kovalainen, fourth on the grid, had to start last after stalling before the formation lap.
Hamilton was sandwiched between the Ferraris after moving ahead of Raikkonen in a clean start for the 20-car field.
Showers picked up and shooting spray had lap times nearly 20 seconds slower than Saturday's qualifying and Hamilton pitted six laps in after his right rear tire brushed the wall.
David Coulthard lost control of his Red Bull car for the second straight day to crash out before Toro Rosso's Sebastien Bourdais reared into him to bring out the safety car for the first time. Six drivers would retire as the 78-lap race was transformed into a clock countdown with Hamilton in front at the end.
Raikkonen was then dealt a drive-through penalty for not fitting his tires in time to start the race and the Finn dropped to fourth behind Hamilton, with Kubica trailing Massa.
Hamilton, who won a wet Japan GP last year, was 17 seconds ahead with half of the 78-laps raced.
With the track drying out, Hamilton set another fastest lap - three seconds better than Massa - to push out. The McLaren driver was clear with only the weather to worry about after a quick pit after 54 laps and the dry tires fitted.
Hamilton's friend Sutil provided the heartbreak and tears, the German starting 18th for Force India but enjoying the race of his life in fourth place until Raikkonen misjudged his braking and shunted him out at the tunnel exit with the checkered flag less than 10 minutes away.
"It was a great race with an incredibly sad ending," said the distraught German.
"We could have had fourth place. It's incredible bad luck that Kimi crashed into me. He obviously didn't do it on purpose."
The glamour of Monaco's race carried into the pit lane with film director Quentin Tarantino, actress Michelle Yeoh, entertainment mogul Sean "P. Diddy" Combs and tennis star Boris Becker all on hand.
(Agencies via Shanghai Daily May 26, 2008)