Red Bull driver Vettel struck early in the final part of qualifying to take his fourth straight pole at Suzuka with a lap of one minute 30.839 seconds.
It is Vettel's 34th in all, moving him to an outright third on the all-time list behind only Michael Schumacher and Ayrton Senna.
But, shortly after the session finished, Vettel and championship leader Alonso, who set the seventh-fastest time, were summoned to appear before the stewards to investigate allegations he had baulked the Spaniard at the chicane during the final moments of qualifying.
A grid penalty would have dealt Vettel's title hopes a blow, but the reprimand means he will lead the field away at the start of Sunday's 53-lap race with Red Bull the dominant force thus far this weekend.
Mark Webber made it an all-Red Bull front row while home hero Kamui Kobayashi will start third for Sauber as McLaren's Jenson Button, who set the third fastest time, serves a five-place grid penalty for a gearbox change.
But World Championship leader Alonso, who holds a 29-point advantage over Vettel, will only start sixth as Ferrari's recent struggles continued.
It was a bitterly disappointing day for Lewis Hamilton, on a weekend dominated by his move to Mercedes for 2013. He will start behind Button even with his team-mate's penalty.
Hamilton radioed his team in Q1 to tell them he felt he was in for a "struggle" and it proved to be the case as he could only manage the ninth fastest time, putting a dent in his own hopes of closing his 52-point deficit to Alonso.
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As a result of Button's grid drop, Romain Grosjean will line up fourth in the leading Renault with new McLaren signing Sergio Perez underlining Sauber's pace this weekend as the Mexican secured fifth on the grid.
Alonso will start sixth as he benefits from Button's penalty, but the Spaniard will be concerned as Ferrari find themselves off the pace of Red Bull and McLaren for the fifth race in a row.
Kimi Raikkonen, who had a spin at the Spoon Curve late in Q3, will line up seventh ahead of the two McLarens.
Force India's Nico Hulkenberg was 10th fastest but he also serves a five-place grid penalty after his gearbox was changed following an off in final practice on Saturday morning.
Felipe Massa could not repeat his impressive performance in morning practice as he failed to get into Q3 with Paul Di Resta and Michael Schumacher next up, although the seven-time champion is another driver serving a penalty. The German's 10-place drop will see him start on the back row of the grid.
Schumacher, who announced his retirement at the end of the season on Thursday, had only just scraped into Q2 with a last-gasp lap after opting not to try a set of soft tyres.
Pastor Maldonado headed Nico Rosberg as Mercedes had a miserable qualifying followed by the Toro Rosso pair of Daniel Ricciardo and Jean-Eric Vergne.
Vergne may yet face sanction from the stewards after Bruno Senna complained bitterly that the Frenchman had blocked him on his flying lap in Q1, meaning it was the Brazilian who was eliminated and not the Toro Rosso man.