The Briton guided his Mercedes expertly around Barcelona’s Circuit de Catalunya to best the Red Bull of Max Verstappen by just 0.036 seconds to bring up three figures.
And Valtteri Bottas, under pressure after speculation that he could be replaced mid-season, took third for Mercedes ahead of the Ferrari of Charles Leclerc.
Five thousand and 82 days have passed since Hamilton took his first pole in only the sixth appearance of his Formula One career at the 2007 Canadian Grand Prix.
Despite being a phenomenal talent, few then would have predicted quite the heights the fresh-faced 22-year-old from Stevenage would go on to reach.
This year, bidding to win an unprecedented eighth world title, his ton of poles takes him 32 clear of Michael Schumacher and 35 ahead of his boyhood hero Ayrton Senna in the all-time list.
Indeed, the numbers are staggering. Hamilton now has two more poles than the combined efforts of double world champion Jim Clark, four-time world champion Alain Prost and 1992 title winner Nigel Mansell.
“We have been strong all weekend,” said Hamilton, 36.
“I cannot believe we are at 100. It is down to the men and women back at the factory who are continuing to raise the bar.
“It has been a dream to work with these guys. I am humble and I am ecstatic, like it is my first.”
Verstappen, eight points behind Hamilton in the standings, said: “It was a good lap. Q3 was pretty decent but the second run was worse for whatever reason.
“Second for us is very good today. We know they are difficult to beat but being close is important. The pace is there so I hope we have a good race.”
Sir Jim Ratcliffe, one-third owner of Mercedes, watched the qualifying drama unfold alongside team principal Toto Wolff, and Britain’s richest man provided the lucky charm for Hamilton.
Verstappen headed into Q3 as the favourite to secure top spot before Hamilton powered his way around the 16 corners and 2.9 miles of Circuit de Catalunya asphalt to steal the glory.
Hamilton is unbeaten on Spanish soil since he collided with rival Nico Rosberg at the fourth turn of the opening lap in 2016.
Verstappen went on to win in his maiden appearance for Red Bull, but pole is key in Barcelona with 22 of the last 30 winners starting from the front slot on the grid.
Behind the top three, Ferrari’s encouraging signs of improvement saw Leclerc finish fourth, with Carlos Sainz sixth in the other scarlet car.
Esteban Ocon qualified fifth for Alpine, with McLaren’s Daniel Ricciardo seventh and Sergio Perez eighth, one second slower than Red Bull team-mate Verstappen.
Lando Norris is third in the standings after a strong start to the season and the British driver will start ninth on Sunday.