The Barcelona-bound 21-year-old, who has often struggled at international level despite his billing as the next great Brazilian player, set the hosts on their way with a stunning volley in the ninth minute, the second game in a row that he has got them off to a flying start.
He repeatedly tormented the Mexican defence and brought the crowd to life with his often cheeky trickery before producing the high point of his display deep into stoppage time.
Collecting the ball on the left, he teased the two defenders blocking his way to the penalty area, then somehow slipped between them and laid the ball off for substitute Jo, only called up as a replacement for the injured Leandro Damiao, to score for the second match running.
Neymar's performance lit up an otherwise ordinary display by Brazil, who produced an electrifying opening 20 minutes but only performed in fits and starts after that.
"We faced a lot of difficulties at certain moments of the game," Brazil coach Luiz Felipe Scolari, whose side have won both their Group A matches without conceding a goal, told touchline television reporters.
"We lost ourselves for 15 minutes, we lost concentration at certain points and that's something we have to correct. But I want to emphasis this Brazilian spirit which we experienced in Fortaleza."
The game was played against the backdrop of protests which have rocked Brazil in the last few days.
There were demonstrations outside the stadium before kick off with protestors demanding "health, education, not corruption".
The nationwide protests were sparked last week by transportation fare increases, which came as Brazil struggles with annual inflation of 6.5 percent, unleashing a tide of complaints that caught authorities off guard.
Contrasting the country's high taxes with its ramshackle schools, hospitals and other government services, demonstrators have criticised the 28 billion reais ($12.9 billion) of public money being spent on preparations for the 2014 World Cup, to be played in 12 Brazilian cities.
The Confederations Cup is a warm-up for next year's tournament.
Inside the stadium, fans enthusiastically sang the national anthem and some held up signs saying: "This protest is not against the national team but against corruption."
Before the match, Neymar surprisingly spoke up in favour of the protestors, an unusual move for footballers who usually steer clear of politics and try to say as little as possible.
"I'm Brazilian and I love my country. I have a family and friends who live in Brazil. For that reason, I want a Brazil which is more just, safer, healthier and more honest," he said on Facebook.
"The only way I can represent and defend Brazil is on the pitch, playing football. From now on, I will enter the field inspired by this movement."
Playing at the stadium where they suffered their last home defeat, against Paragua
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