For Vettel to be crowned for a second time at Suzuka, as was the case two years ago, he enjoyed the ideal scenario come the conclusion to practice.
Vettel heads into the weekend knowing if he wins a fifth successive race - after recent successes in Belgium, Italy, Singapore and Korea - and Alonso finishes ninth or lower, he will again be champion.
Unsurprisingly, the 26-year-old finished top of the timesheet at the end of the two 90-minute sessions under clear blue skies and with temperatures pushing 30 degrees.
As for Alonso, the Spaniard was down in a miserable 10th, 1.235secs adrift, but more worringly behind Toro Rosso's Daniel Ricciardo who was seventh and Jenson Button in his McLaren, with the Briton ninth.
A disappointed Alonso, 77 points adrift of Vettel and standing in the last-chance saloon when it comes to his championship chances, said: "In terms of competitiveness, we are not in the position we wanted.
"We definitely need to improve because we were not at a good level, so now we must try and improve. We need to raise our game.
"Mercedes, Red Bull, Lotus, they are in front of us, and they should be in front of us.
"But we have Ricciardo, we have the McLaren, people that are normally behind us are now in front.
"We hope to get a clean lap in qualifying (on Saturday) to be ahead of those cars that we cannot have in front of us."
Alonso did not help his own cause, though, as he was one of many who suffered an incident on a track widely regarded as arguably the best in F1, but also the most unforgiving.
Whereas many current circuits have considerable run-off areas to aid a driver when he makes a mistake, Suzuka has many gravel traps.
Alonso was fortunate to avoid one as he spun on the approach to the second Degner curve that caught out Marussia's Jules Bianchi, Giedo van der Garde in his Caterham and Williams' Pastor Maldonado.
Alonso added: "We didn't extract the maximum, but I also made a mistake with a spin. Things were not good enough.
"Luckily, when I spun I didn't ruin the tyres. We also managed to use them on the long run with a full fuel load, even if we definitely lost a few extra tenths from the first lap.
"We must now put together a series of changes we have in mind and do a good lap in Q3 (the final part of qualifying) because it's important to start from the front."
Overall, Vettel finished 0.168secs ahead of Red Bull team-mate Mark Webber, with Nico Rosberg a quarter of a second down in his Mercedes.
The leading trio were followed by Lotus' Kimi Raikkonen, who did find a gravel trap that brought his second session to a close 35 minutes early.
The Finn was narrowly ahead of team-mate Romain Grosjean, with Lewis Hamilton only sixth in his Mercedes and with a time three tenths of a second slower than his leading best in first practice.
Despite that, Hamilton was relatively satisfied as he said: "I'm happy with where our car is after the first practice sessions.
"Of course, we would love to be more competitive, but we've some work to do on the tyre management in particular.
"It's too early to think about what we can achieve, but I'm looking forward to a competitive qualifying and then we will have to see what we can do in the race."
Force India's Paul Di Resta, one of many who suffered a minor spin, was 14th, just 0.066secs ahead of team-mate Adrian Sutil.
For a driver whose F1 future is in doubt, McLaren's Sergio Perez did himself no favours by slamming sideways into a tyre barrier at one of Suzuka's renowned turns, the Spoon Curve.
Maldonado's accident in FP2 was not the Venezuelan's first as he also lost his left-rear wheel in FP1. An investigation discovered it had not been securely fastened, resulting in Williams being fined 60,000 euros (£50,852).