Prince Charles and Camilla Parker-Bowles had a televised religious blessing there after they had a civil wedding ceremony nearby in 2005.
They are grateful to the Queen for granting permission for the use of the chapel.
Harry, who is fifth in line to the throne, and American actress Markle have been dating for about a year and a half.
Based on Meghan's Instagram photos, the trio were in Spain in August, which means they could have easily been in London in July, when Prince Harry and Meghan met.
Officials also confirmed that Markle will be baptized and confirmed in the Church of England at some point before the wedding. The Queen is the head of the Church of England. St. George's Chapel seats 800 while Westminster Abbey can fit a whopping 2,000 people.
However, it is on the Windsor Castle estate, and will be more hard for members of the public to access. She will join Prince William, Kate and Prince Harry's royal foundation as its fourth patron, and work with her husband to support causes close to her heart.
It is not yet know how the public might be able to view either the wedding or the potential arrival of the bridal party at the chapel.
Ms Markle, 36, and Prince Harry, 33, formally announced their engagement at Kensington Palace, their home, on Monday.
Image Prince Harry and Meghan Markle will marry next May
The bride-to-be will also become a United Kingdom citizen but the process could take a number of years.
St George's Chapel. Formal but not too formal.
In Nottingham, the pair will visit the Nottingham Contemporary which is hosting a Terrence Higgins Trust World Aids Day charity fair, and also visit Nottingham Academy to meet headteachers taking part in the Full Effect programme.
"Bogart is now living with friends", Mr Knauf revealed.
"As you can see, they are so happy."
A May date will avoid a clash with the arrival of Prince William and Catherine's third child, which is due in April.