The Venezuelan was well-placed to take advantage of an off-track moment by poleman Tom Dillmann at the Turn 13 hairpin, shortly after a restart, on lap 13.
Once ahead, Cecotto Jr extended a 2.2s margin of victory over AVF racer Dillmann, whose second place provides him with a one point lead in the drivers' championship over Louis Deletraz.
"This result is fantastic for the whole team," said Cecotto Jr. "We had a few issues in the first free practice session, but then in FP2 we were leading the pace.
"I was sure we could have started on the front row, but we made a mistake in strategy in qualifying. The race pace was really strong through, and I could take advantage when Tom made a big mistake."
Aragon winner Deletraz harried Dillmann to the finish, but was unable to stage an overtaking attempt on his vastly more experienced rival.
"I made a good start, and tried to open up a gap, thinking I could save my tyres later in the race," explained Dillmann.
"Unfortunately, we had the safety-car. My restart was actually good, but I should have waited longer until braking late as things weren't quite up to temperature. I am really disappointed for the team. I am not thinking about the championship at the moment, my goal now is to go after race victories."
Deletraz's task in wrestling the runner-up spot was made decidedly more difficult by a fuel leak that was discovered on the out lap to the grid.
"I told the guys that I could smell fuel, and it felt like something was burning," said Deletraz. "I got out of the car and we discovered that the cockpit was full of fuel.
"I was worried that it might be dangerous to attempt to race, but we said that we would try. It was really painful. All I could do was try to forget about it. I think in the circumstances this podium is a good result."
The top-three finished a commanding 11s clear of a tight scrap for fourth, disputed between Aragon winner Aurelien Panis and Matthieu Vaxiviere.
The confines of the Hungaroring increased the challenge of overtaking, and 2015 Formula Renault 3.5 runner-up Vaxiviere had to settle for fifth, 0.7s in arrears.
Aragon pole winner Egor Orudzhev's charge through the field from his 13th place grid slot ended in the Turn 6 gravel trap, after the SMP-backed Arden racer tangled with an overly-defensive Alfonso Celis Jr.
The Force India Formula 1 Friday practice driver had run marginally wide at the preceding corner, presenting Orudzhev with an opportunity to gain an overlap and attack the AVF car's inside.
The Mexican then appeared to move across the road and squeeze Orudzhev, before contact was made.
The incident would influence the outcome of the race, as it triggered the deployment of the safety-car and negated Dillmann's 2.7s lead on lap 10.
Dillmann leads the standings on 51 points, one ahead of Deletraz. Aurelien Panis is third on 47, while Johnny Cecotto Jr's victory moves him up to fourth.
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