instantaneous acceleration is measured over a "short" time interval. The word short in this context means infinitely small or infinitesimal — having no duration or extent whatsoever.
It's a mathematical ideal that can can only be realized as a limit. The limit of a rate as the denominator approaches zero is called a derivative.
Instantaneous acceleration is then the limit of average acceleration as the time interval approaches zero — or alternatively, acceleration is the derivative of velocity.