Yes, the marriage certificate could be used as evidence in a spouse visa application. It will be an official marriage certificate (same to getting married at your local courthouse).
Note: Some U.S. attorneys also say that the couple must “consummate” the virtual marriage afterward, meaning they need to be together in the same physical place at some point after the virtual marriage and before applying for the visa. This is usually proven by providing documentation such as photos together, plane tickets, and hotel reservations. We are not a law firm – you may want to talk to a U.S. immigration lawyer.