To refill by one, select the Reserve Tank and press up on the same frame (right or down can instead be used if Samus has items in those locations).
To do this again without unpausing is requires a down and up input on consecutive frames, which is unreasonable.
Alternatively, if Samus has items on the right column, pressing down and right on consecutive frames works.
This can be useful for getting exact Reserve Energy for setting up G-Mode, or to pause abuse multiple times with minimal Energy loss.
See also: Tech Page