First, to be clear, I agree with conclusions from others: no, they will not count this as physically present, and whatever registration procedure you did later in a different country doesn't magically make it a physically present ceremony via time travel or whatever.
I'd add: my impression is that IRCC may not pay as much attention to these US-online marriages for US citizens and (permanent) residents. That's only a guess though.
Now a question: what country was this registration procedure, and what is the 'marriage certificate' called? I think there is only a tiny, tiny chance that this marriage certificate would be considered evidence of a distinct marriage (i.e. de novo), but specifics would matter.
Otherwise I believe the options are to carry out a new marriage - after a divorce ideally, but would guess that from IRCC's perspective, they can't object to a new marriage if they consider the first one invalid/null and void/never happened. The problem is that other jurisdictions that consider the first marriage valid may (logically) refuse to carry out a new one. (Leaving aside whether one could simply not mention that and whether there could be any consequences to not doing so - to which the answer is probably not)
Important to note that you've asked this in the family sponsorship forum, and your case is NOT family sponsorship - even fixing this may not get the SOWP approved, and even more so if the timing is sensitive.
I am in a similar situation if you do not mind me asking. I have not gotten married yet but I'm trying to find the quickest way to get married while not in the same country with it being recognized. If we both got married virtually while in the same country would this be acceptable? My brain is spinning trying to wrap my head around the "in person" part of it. Because technically we would both be together attending a virtual wedding. I am trying to move from the United States to Canada to be with him.