Hamilton's Mercedes team-mate Valterri Bottas, who won his first Grand Prix last time out in Russian Federation, is third in the championship, 10 points behind the British driver.
Carlos Sainz Jr. finished 12th for Toro Rosso ahead of Nico Hulkenberg in P13, while Pascal Wehrlein took P15 for Sauber after squeezing through to Q2.
Sebastian Vettel ended the session in second place, just 0.051 seconds behind Hamilton's Mercedes, but things could have been a lot worse for the German.
Ferrari fought back against Mercedes in final practice for the Spanish Grand Prix on Saturday with Kimi Raikkonen leading championship leader Sebastian Vettel in a red one-two.
Nico Rosberg, the victor of the first four races in 2016, won the title with Mercedes last season, while Hamilton won the previous two championships.
Hamilton was fastest in 1 minute, 19.149 seconds, with Vettel only 0.051 behind.
Mercedes have a one-point lead over Ferrari in the constructors' championship. Lewis has won 1 out of 4 and placed second in two of the races.
"It will be a tough race for sure when you see how close it is between us", said Hamilton.
"It's the third longest run down to turn one so it's going to be important to get a good start".
Valtteri Bottas's Mercedes team broke the Friday night curfew to fix an electrical fault on his vehicle.
Ferrari's Kimi Raikkonen, who was fastest in third practice, will begin in fourth while the two Red Bull's of Max Verstappen and Daniel Ricciardo will be in fifth and sixth respectively.
The home favourite reached Q3 for the first time this season and secured seventh position, opening a chance for him to score some points before skipping the Monaco Grand Prix to take part in the Indianapolis 500.
Hamilton had topped the times in both sessions on Friday to encourage Mercedes to believe that their upgrades package had brought them back to the front of the pack. Hamilton went out and did just that, although it seems the two rival teams are neck and neck once again.
It is too early to make any conclusions about relative pace, not least because Vettel's session was disrupted by a gearbox problem on the pit straight.
"It's a miracle that they got me out". I wasn't always feeling like I was captain on-board. "Much better in terms of feel today". "In terms of performance, it will be really close".
"The fans here are wonderful every year and I feel like I've really been grown a lot in Spain in the last ten years so I really appreciate all of the support I get here", said Hamilton after taking his 64th Formula 1 pole.
Hamilton and Vettel both pointed to the unpredictable gusts of wind - in otherwise ideal sunny conditions - that have troubled drivers all weekend.