The Paris Saint-Germain superstar took the prize despite missing the last three months of the season due to injury.
Neymar moved to PSG last summer from Barcelona for a world record record fee of £198m last summer, and after scoring 26 goals in 29 appearances in his debut season, he was sidelined by foot injury since late February.
"I was not supposed to play in the match [Troyes away in Ligue 1] just after the two Marseille games", Neymar said.
Neymar has missed the second half of the season with PSG after injuring his metatarsal, but the Brazilian should be fit for his national side's World Cup campaign in Russian Federation this summer.
Paris: Neymar's doctor Rodrigo Lasmar said on Friday that the injured Brazilian star could return to training as early as next week if he responds well to scheduled tests on Saturday.
Alves limped off near the end of Tuesday's French Cup Final win over third-tier Les Herbiers.
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"We will be in Russian Federation to play something very important", he said. "There's no need for me to want anything else for him".
Asked whether Neymar will be at PSG next season, Al-Khelaifi said in quotes reported by Le Parisien: "For me, for Neymar, I am 2,000 per cent sure he will stay". There was buzz about him not getting along with teammates, which we actually kind of saw with Edinson Cavani, and it felt as if his time at PSG could come to a quick close.
Real Madrid believe they are frontrunners to sign the 26-year-old, who shocked the football world by agreeing to join PSG from Barcelona last summer for a staggering £198m. And then he arrived at the locker room and said: "'Well, I saw you dribbling and I tried to do the same!'"
The 23-year-old has generally impressed whenever used by PSG, though he hasn't quite been an established starter week in, week out for the French giants.
"He's a phenomenon. I've already told (Brazil midfielder) Casemiro that he'll have to take care of him" if Brazil face France in Russian Federation.