Ivana drew her last game against Zansaya Abdumalik to total nine points from 11 rounds, half-a-point more than Azerbaijan's Gunay Mammdzada, who had to be content with a silver.
Pint-sized Ivana had the better of Zhansaya Abdumalik of Kazakhstan and was in a winning position, but agreed for a draw, which still gave the Indian the title.
Shalmali beat Poland's Katarzyna Adamovicz to pocket a bronze medal in the U-14 category. Prince Bajaj drew with Mikhail Antipov that enabled him to claim the bronze.
Bajaj-Antipov game lasted just 12 moves. With both players being assured of a medal with a draw, they quickly opted to split the point.
India, with three medals, finished joint third along with Ukraine, Azerbaijan and Georgia. Russia won the championship with nine medals followed by China with five.
It was a sharp fall from the last year's haul, when India had claimed record 10 medals, including five gold, two silver and three bronze, in Batumi, Georgia.
In U-18 girl's section, another Indian Mary Ann Gomes lost to eventual winner Valentina Gunina of Russia in the last round.