Although the link between motor synchrony and emotional alignment has been extensively studied during face-to-face interaction, the question of whether this association also exists in virtual settings has remained unanswered. Here, we examined whether this link exists during virtual social interactions and whether pro-social effects will be induced during those interactions. To this end, two strangers shared difficulties they have experienced due to the COVID-19 pandemic during a virtual social interaction that included both audio and video. The findings revealed that motor synchrony and emotional alignment can arise spontaneously during a virtual social interaction between two strangers. Moreover, this interaction yielded a decrease in negative affect and an increase in positive affect, as well as an increase in feelings of trust, liking, cohesion, self-other overlap, and similarity between the strangers. Finally, a higher level of synchrony during the virtual interaction was specifically associated with increased positive emotional alignment and liking. It can thus be presumed that virtual social interactions may share similar characteristics and social effects as face-to-face interactions. Considering the tremendous changes the COVID-19 pandemic has caused regarding social communication, these findings may provide grounds for developing new intervention protocols aimed at dealing with the consequences of social distancing.