With both Alonso and team-mate Felipe Massa starting on the dirty side of the grid at the Circuit of The Americas, Ferrari opted to break the seal on the latter's car, so incurring a five-place grid penalty.
That allowed Alonso to move up from eighth to seventh, whilst Massa dropped back to 11th from sixth, but with both on the clean side to allow for greater traction off the line.
It proved a successful move as Alonso had launched himself up to fourth coming out of the first corner, eventually finishing third behind championship rival Sebastian Vettel who was runner-up, whilst Massa was fourth.
That at least allowed Alonso to limit the damage to Vettel, who has a 13-point cushion going into Sunday's season-ending Brazilian Grand Prix.
Asked if he would be comfortable winning the title on the back of such a move, Alonso replied: "I am proud of my team for the strategy decision to start on the clean side with both cars.
"It worked quite well and perhaps because it worked well maybe that is why rivals are not happy.
"I am also proud of my team because they told the truth. Not every team has told the truth when they have made strategic decisions."
The likes of McLaren's Martin Whitmarsh and Eric Boullier at Lotus both called into question Ferrari's decision.
Whitmarsh admitted he would have been angered if he had been boss of one of the teams whose cars was switched from the clean to the dirty side.
One of those was Force India's Nico Hulkenberg, however, deputy team principal Bob Fernley said he would have done exactly the same thing if in Ferrari's position.
Alonso claimed it to be "funny" the reaction from some teams, suggesting it to be hypocritical.
"I think we have seen so many things coming from the teams, not only this year, but also in the past in F1," added Alonso.
"We don't need to go too far with some of the races where we had some doubts, even on Saturday night, about which teams and which position they were starting depending on some decisions."
Vettel is convinced Red Bull would have not gone down the same route.
"What they (Ferrari) do is not in our hands," said Vettel.
"I didn't follow up whether Felipe had real trouble with the gearbox or not, but it is not our job to focus on these things.
"It is a different approach compared to our team. That is how life is. Everyone handles certain situations in a different way."
Brazilian Grand Prix Air Times (SGT/HKT)
Practice 1: Fri 20:00
Practice 2: Fri (Saturday) 00:00
Practice 3: Sat 21:00
Qualifying: Saturday (Sunday) 00:00
Race: Sunday (Monday) 00:00