Even with a scruffy second flying lap, Hamilton pipped Bottas by +0.059 seconds on the first run of the session to secure his 92nd career pole position.
With Verstappen seven-tenths behind in third for Red Bull, Hamilton applauded the work ethic of the team, despite their current dominance.
Speaking after securing pole, Hamilton said: "[The second lap] wasn't a great lap.
"The first one was decent which did the job thankfully. These guys have done such an awesome job. We are constantly learning.
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"I was here with the guys until 10 pm last night looking over all the details, how can we improve, what are the areas, particularly for the race, that we can get better because these Red Bull's are super fast.
"This is the first time I have been here in Barcelona when it has been this hot. Physically it is tough, it is so fast around here. It is the fastest we have ever been round here so the forces through the body is pretty intense but the tyres are what we are really struggling with.
"You see us crawling around on the out lap just to keep the temperature out of the tyres. Even with those slow laps, you have temperatures rising. That is what we try to manage on the laps. "
The two Mercedes drivers battled each other during the opening lap of the 70th Anniversary Grand Prix last week and Hamilton is aware he needs a perfect start to fend off his rivals behind.
"This is such a long way down to turn one here," he added.
"The job is not done, that's for sure. It is very hard to follow here. Positioning is good. It will be hard to hold position but that is what I have got to work on and try and get the best start I can."
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