Can humans ever directly see a few photons at a time? Can a human see a single photon?
A single molecule of rhodopsin (actually the cis-retinal bound to it) can and actually does react to one photon (Purves et al. Chapter: Phototransduction in Neuroscience). 


  It has been estimated that a single light-activated rhodopsin molecule
  can activate 800 transducin molecules, roughly eight percent of the
  molecules on the disk surface. Although each transducin molecule
  activates only one phosphodiesterase molecule, each of these is in
  turn capable of catalyzing the breakdown of as many as six cGMP
  molecules. As a result, the absorption of a single photon by a
  rhodopsin molecule results in the closure of approximately 200 ion
  channels, or about 2% of the number of channels in each rod that are
  open in the dark. This number of channel closures causes a net change
  in the membrane potential of about 1 mV.


Photoreceptor cells continuously secrete the neurotransmitter glutamate in dark; with light exposure glutamate release would reduce. This leads to activation of the next line of cells (bipolar, horizontal cells and retinal ganglion cells).


  
   Modelled relationship between glutamate release and rod membrane potential.  From Witkovsky et al. (1997).


From this model (Witkovsky et al. 1997) it appears that for a change in glutamate release rate, a larger change in membrane potential is needed. Moreover, the depolarization of the photoreceptors has to be sustained for a while so that downstream cells can react (light absorption is much much faster than biochemical processes). The lifetime of an activated rhodopsin molecule is ~40ms in mice (Gross and Burns, 2010) and ~400ms in salamanders (Lyubarsky et al., 1996). We can assume that human eye is more similar to that of mice. There are approximately 40,000,000 molecules of rhodopsin in a rod cell (BioNumbers). The most sensitive of retinal ganglion cells need ~0.04% of rhodopsin molecules per rod cell to be activated (Takeshita et al., 2017).


  (b) Absolute threshold of On and Off retinal ganglion cells
  
  Both On and Off RGCs carry rich information about the weakest light
  signals. Off cells are somewhat more sensitive than On cells but have
  a higher error rate in their gap-based coding. The absolute threshold
  for primate On and Off parasol cells in a two-alternative
  forced-choice task is extremely close to the limits posed by the
  quantal nature of light: On parasols reach 75% correct choices at a
  light level corresponding to approximately 0.0008 R* per rod per flash
  (mean, n = 6) and Off parasols at a light level corresponding to
  approximately 0.0004 R* per rod per flash (mean, n = 5).


A single activated rhodopsin molecule would be 0.0000025% of the total. This would be insufficient to activate an RGC.

So, I can make a reliable guess that you cannot actually "see" a photon although one of the retinal photoreceptor cells can sense it. However, I'm still looking for a solid reference that says how many photons are needed (and for how long) to produce a visual response.