Yoanka, with 18 points, was behind of Dutch Marien Vos, who obtained 30 points to win the gold, while Spaniard Leire Olaberría, 13, finished in the third position.
The Cuban cyclist, 32, substantially improved her performance in Athens four years ago, when she finished 10th.
This was a good day for Latin America, because besides Yoanka's silver, Colombian Maria Luisa Calle finished in the fourth position with identical score to the Spaniard, but the last one won the sprint.
Yoanka, fifth in the world ranking, gave Cuba the chance of becoming the eighth country to win a medal in the cycling championships of these Olympic Games.
Gonzalez' medal is something unprecedented in a competition usually won by the Europeans and confirms what she said before leaving Havana for Beijing that escorting the Cuban flag will give her the strength to return with a good result.