The 23-year-old, who was a fifth-round pick for the Vikings in the 2019 draft, made five appearances in his rookie season for the franchise, recording eight tackles.
"Earlier this week I found out I need open heart surgery to fix a bicuspid aortic valve that I was born with," Smith wrote on Instagram.
"Although this will unfortunately end my 2020 season, it is really a blessing that we found this as my heart is severely enlarged and wouldn't have lasted much longer.
"I found this out after I tested positive for Covid and had to have further testing done as protocol. The Lord works in mysterious ways, but I could really feel him on this one!"
Smith has opted for a procedure that will allow him to make as swift a return to action as possible.
"There is a surgery that will allow me to continue to play football as soon as I am healed and cleared and I didn't think twice about going with that one," he added.
"By no means am I ready to be done playing football, there is still so much more I want to accomplish on the field.
"I'm going to attack this like everything else I have in life. Already looking forward to the comeback!"