Team mate Valtteri Bottas took second place while Red Bull's Max Verstappen took third place after a botched pit stop ruined Sebastian Vettel's chance of making podium during a virtual safety vehicle stint. It capped off a disappointing afternoon for Ferrari, who saw Kimi Raikkonen retire after suffering a loss of power with a brand new engine which had been fitted to his vehicle on Saturday morning.
Kimi Raikkonen finished in fourth place for Ferrari, ahead of the Red Bull duo of Max Verstappen and Daniel Ricciardo.
Today the vehicle and myself, I felt that synergy which I hadn't been feeling for the whole year.
Valtteri Bottas backed up Hamilton's win with second place to give Mercedes maximum points, and the Finn added that his disappointment at being beaten by his teammate is tempered by the team's performance.
Verstappen, whose season has been littered with collisions, also almost wrecked his race when he hit the rear of Canadian Lance Stroll's Williams and lost a front wing end-plate. "I've not had pole for a while", Hamilton said.
Bottas claimed his first Spanish Grand Prix podium, while Verstappen's race was compromised late on when he damaged his front wing running into the back of Williams' Lance Stroll. "And I think Fernando may still be suffering from things that happened ten years ago, even if he is a different person now".
Hamilton was never challenged on the way to his 41st win from pole position, surpassing a record he shared with seven-time world champion Michael Schumacher.
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The leading cars navigated the opening metres without drama before the error-prone Romain Grosjean, once labelled a "first-lap nutcase" by Mark Webber, lived up to that title by sparking a huge crash after he lost control of his Haas at Turn 3 and slid back across the track in a cloud of tyre smoke.
The safety auto has helped add to the drama of the early part of the 2018 season and its appearance early in Sunday's race means it has been used in the opening five races of a championship for the first time.
Vettel said he was "not entirely happy" but already expected Mercedes to be strong. Vettel won in Australia and Bahrain, while Ricciardo was first in China and Hamilton triumphed in Azerbaijan.
In total, six cars failed to finish.
Ferrari surrendered the lead in the constructors' championship to Mercedes and now trail them by 27 points after five races. This is hard to cope with and in the following races we struggled and all that adds up and was in all our minds. He had a spin shortly after the Ocon-induced virtual safety vehicle. What had looked at first sight like questionable strategy was actually, they said, just the vehicle going through its tyres quicker than others.
Ferrari's Sebastian Vettel (right) after qualifying third for Sunday's Spanish F1 Grand Prix. After retiring in Baku, the Frenchman was full of optimistic coming in to Spain, but was forced to retire on lap 44 due to power failure.