Sebastian Vettel hadn't looked likely to claim pole position until the very final seconds of Q3, when he was able to pop into the top spot with a lap of 1:30.466s after timing his final run to perfection.
Running just behind him, McLaren's Jenson Button - who had topped the timesheets for every session going into qualifying - was just 0.009s too slow in his final run in his efforts to keep the Red Bull off the pole.
But the story of Q3 was Lewis Hamilton's failure to start his final flying lap before the chequered flag came out, after Mark Webber passed him on the warm-up lap which resulted in Hamilton easing up to find some space. Following close behind, Michael Schumacher immediately realised the danger of them both missing the cut-off at the end of the session. He promptly forced his way past Hamilton at the final chicane in his efforts to make it, but neither man was able to get to the start line in time to make a flying lap attempt.
Before this last-minute drama, it had been a very odd Q3 with teams having to prioritise tyre conservation above all else. That meant that only five drivers - Hamilton, Vettel, Button, Mark Webber and Felipe Massa - had set early fast times, with Hamilton the fastest of the group before activity on the track had gone into a strange lull.
Despite not making his final run, Hamilton's earlier time of 1:30.617s was still good enough to hold on to third place and was just 0.151s behind pole when the session was over, just in front of the two Ferraris of Massa and Alonso. Mark Webber's final lap was compromised by his own mad scramble to get to the start line in time, and he was only able to set the sixth fastest time of Q3.
Teams had been reluctant to throw a new set of tyres at qualifying, given that the race could conceivably require anything up to five pit stops during the course of afternoon in light of the blistering issues that teams have been starting to see at the Suzuka track. Along with Schumacher, three more of the ten drivers in Q3 failed to set flying laps - Bruno Senna and Vitaly Petrov deciding that there was nothing to gain from burning through any further sets of tyres and consequently opting to sit out the session entirely, while local hero Kamui Kobayashi came out for a crowd-pleasing exhibition lap on worn tyres just to give the home crowd an opportunity to go wild cheering for him.
Tyre management had also affected Q2. The top seven front runners took the risk of getting caught out by a late flying lap from one of the midfielders and sat out the end of the session in the pits, while the final three top ten positions were decided in a late flurry that saw Sauber's Kamui Kobayashi thrill his fans by popping up into eighth place, with Senna and Petrov also managing to slip both Renaults through.
Force India was caught on the losing end of the gambit. Despite Adrian Sutil topping the timesheets in the earliest part of Q2, he would end up getting knocked out of the top ten by the time the second round of qualifying concluded. Paul di Resta only had one flying lap attempt and could manage just twelfth place.
After their torrid Friday, the Williams duo of Rubens Barrichello and Pastor Maldonado will be satisfied and probably pleasantly surprised by finding themselves in 13th and 14th on the grid for Sunday afternoon's F1 Grand Prix of Japan. Conversely, Toro Rosso's Sebastien Buemi and Jamie Alguersuari will be disappointed to end up in only 15th and 16th positions.