Alonso's lead was less than a second for most of the race, in which he drove astutely to ensure his rivals were never quite close enough to try to pass.
Ferrari team boss Stefano Domenicali said: "It's true [we don't have the fastest car]. If we did, it would be easier to win.
"We need to improve the car. We need to make sure our car is good in all the different conditions - wet, dry, different kind of tyres and so on. It is such a tight championship you need to make sure you can develop the car race by race."
Alonso is 44 points ahead of Vettel, with Lotus driver Kimi Raikkonen fourth, 56 behind.
Red Bull team boss Christian Horner said: "Fernando has finished all the races in the points - he has a 34-point lead, but that isn't insurmountable with 25 points for a win.
"It's important we get both of our guys beating him. He's been driving incredibly well, he's hit a purple patch of form. But we'll be looking to put as much pressure on as we can in the second half of the year.
"The [Ferrari] car has come on in leaps and bounds, but there is an awful lot of racing to be done between now and the chequered flag in Brazil [at the final race of the season]."
McLaren's Lewis Hamilton has slipped to fifth in the championship, 62 points behind Alonso, after retiring from the German Grand Prix with a gearbox problem caused by an early puncture.
Button is seventh, 86 points behind, but Horner said even he could not be ruled out.
1) Fernando Alonso - 154
2) Mark Webber - 120
3) Sebastian Vettel - 110
4) Kimi Raikkonen - 98
5) Lewis Hamilton - 92
6) Nico Rosberg - 76
7) Jenson Button - 68
8) Romain Grosjean - 61
"I don't think you can write off anybody in this championship," Horner said.
"People were saying Jenson's had a bad run; he drove a great race today.
"I think it would be unwise to write off any of the top six guys at the moment.
"It only takes a couple of DNFs for Fernando or any of the front guys and the picture can change quickly if you hit a bit of form."
McLaren team principal Martin Whitmarsh said: "We're at the halfway point and we have a lot of racing ahead of us, and they can both do it.
"This season is going to be right to the very end. I believe we will be sat on the edge of our seats in the last few laps of the Brazilian Grand Prix and I hope I am in deep agony on those laps because it means we are in contention to win.
"Fernando is doing a great job and so are Ferrari. They are difficult to beat but it's doable. We are a motor racing team, we are fighters and we have to concentrate on, race by race, trying to maximise points and see if we can erode that situation.
"It's going to be a great, great season. It already has been a great season.
"Coming out of [the first race in] Melbourne you'd have said we were on a roll and they [Ferrari] were in trouble.
"You've got congratulate them. We're on the pace now, we just have to keep pushing, keep the faith, keep focused, don't make mistakes and I think both our drivers are capable of winning races and they are both still capable of winning the world championship."
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