Jake Dennis (Fortec Motorsports) and Stoffel Vandoorne (Josef Kaufmann Racing) were also on the podium.
Andrea Pizzitola had secured pole position in qualifying for the second race but dropped back from the start and finished 13th.
A big crash involving Norman Nato (RC Formula), Victor Franzoni (Koiranen Motorsport), Stefan Wackerbauer (Koiranen Motorsport), Dan de Zille (Fortec Motorsports), Yu Kanamaru (KTR), Oscar Tunjo (Tech 1 Racing), Matthieu Vaxivière (Tech 1 Racing) and Javier Tarancon (RC Formula) brought out a red flag.
However Kvyat, who was leading at the time, got away well and saw out the win.
“The race conditions were very difficult, and I knew it was important to get away in front at the start,” said Kvyat.
“I took risks and they paid off. It was nervy and it wasn’t easy to manage things while the race was interrupted.
“I benefited from having better visibility than the others, and this made the difference. It’s an important victory after my relatively below-par performance in the first race.”