Taking his tally to an impressive seven points out of a possible nine, Harikrishna made his tactics work again and Nyzhnyk had no clue what hit him in the finale.
The victory also took Harikrishna's performance rating above 2800 levels, something that is rarely achieved after nine rounds.
D Harika, however, did not have such a good day and was caught in what seemed like a home-preparation by Erwin L'Ami of Holland. The Indian remained on three points.
With just four rounds to come, Alexander Motylev of Russia, Lazaro Bruzon of Cuba and L'Ami share the second spot on six points while the next ranked players are another one and a half points adrift.
These three, along with Harikrishna, will fight for honours but Harikrishna seems far ahead as of now.
In the 'C' group being held simultaneously, it was heartbreak for Indian International Master Sahaj Grover who suffered a shock defeat against Anne Haast of Holland.
Turning the tables from a lost position, Anne Haast made the most of Grover's blunder to also get the best game prize of the day.
Maxim Turov of Russia defeated Tania Sachdev while B Adhiban scored over Pieter Hopman to keep his chances alive.
Turov continues to share the lead with Hans Tikkanen of Sweden on 7.5 points in this section while Adhiban stands third, a point behind.
Grover is still in joint fourth spot on five points in the company of top seed Matthew Sadler of England and Daan Brandenburg of Holland while Tania has 3.5 points in all.
In the premier group 'A', there was a major change in fortunes as Armenian Levon Aronian shot ahead with a crushing victory over Fabiano Caruana of Italy.
Sergey Karjakin of Russia provided the proverbial twist defeating world number one Magnus Carlsen of Norway.
Harikrishna employed the Queen's gambit declined once again showing his peaceful intentions but Nyzhnyk, who is the youngest participant at 15 here, decided to make it a complicated affair by opting for a rare system.
Trading the queens early, Harikrishna capitalised on an oversight by Nyzhnyk and following a well-calculated piece sacrifice, the Indian posted both his rooks on seventh rank. It was all over in just 28 moves.
In other matches, Harika went down in a Grunfeld defense game while Adhiban won a tense game out of a Phillidor defense.
Grover was outdone after missing winning moves out of his pet French defense while Tania did not give adequate treatment to the English opening.