The world championship leader produced a lap of one minute, 16.173 seconds at the Circuit de Barcelona-Catalunya to beat his team-mate Valtteri Bottas into second.
Bottas was just slightly slower than his teammate on his final flying lap, and could have had the pole himself.
It should also be a good chance for Red Bull to bounce back after last race's disaster. But because of Botas' late devastation, along with Kimi Raikkonen's second-place finish, Ferrari jumped ahead of Mercedes in the constructor standings.
While Ferrari - in contrast to Mercedes - usually has no problems to extract the best from the softest tyres, today's session seemed to favour its rival.
A change of strategy perhaps for Red Bull then? Leclerc, running in P8, was proving to be a stubborn opponent for Alonso.
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But Vettel struggled with tire wear and Ferrari made a decision to bring him in for an extra stop.
Stroll almost hit the tire barriers after going off the track with about a half-hour left in the session.
But Vettel said there was no escaping the fact that Ferrari was simply outperformed by Mercedes in Spain.
It didn't say how many subscribers were affected.
There was no messing around from Hamilton at the start of Q3 as he claimed provisional pole on his first lap and never relinquished the position.
"It's great to get a lot of points for the team today". Hamilton was -0.132 seconds on Vettel in Q3 - which one could argue is a sliver. Excuse me, but this is the team Sir Frank Williams and Sir Patrick Head turned into a force that delivered 114 victories through drivers such as Piquet, Mansell and Prost.
Hamilton said: "The vehicle and myself, I felt that synergy that I hadn't been feeling all year". "This is when we are going to start applying some pressure. I was saying to Valtteri (Bottas) when we get to Monaco we'll be driving around with cold tires because it is not easy to get temperatures up there". The team did an exceptional job. "We have found some pace, there is still a bit more to find, but overall a pretty good end to a Friday".
Alonso has now gone five full years without a race victory.