It depends on what G-Sync setting you're using. G-Sync has two modes that it operates in: full screen or desktop. If you're using full-screen, it will only enable when a graphics renderer creates a full-screen window (borderless window does not count). If your player does this, G-Sync should affect it. Although, most people tend to use borderless window for players.
If I remember correctly, on the other hand, the desktop version of G-Sync ties itself to the currently active window's refresh rate.