The emotional athlete, who runs for Ireland, had not been told of his mother Catherine's involvement prior to the ceremony for the T37 1,500m race. He had tears in his eyes as the medal was placed around his neck.
The pair embraced to loud cheers from the crowds at the Olympic Stadium, the outside of which was bathed in green light to honour the Irish athlete. Flowers were given to McKillop by Paralympics veteran Baroness Tanni Grey-Thompson.
It is thought to be the first time a mother has presented her son with a medal at the Games and was organised by Paralympics partner P&G.
Liam Harbison, Paralympics Ireland chef de mission said: "This is a fantastic achievement for Michael. For him to race in front of his mum at this level for the first time is special but to receive his gold medal from his mum will be a memory he will treasure forever. As a supporter of Paralympics Ireland, we are delighted P&G were able to enable an Irish athlete to enjoy such a moment."
Nathan Homer, Olympics & Paralympics Project Director at P&G, said: "This is an extraordinary accomplishment, and on behalf of P&G, I am delighted for Michael, his mum Catherine and family. And to see Catherine hand over a gold medal to her son during such an historic occasion really is something very special that the family can treasure. Congratulations."
Speaking before the medal ceremony, McKillop said of his win: "It feels unbelievable, it feels fantastic to be able to do it in a crowd so big and cheering you on the whole way.
"Even though there was a British guy in my race I felt like they were cheering for me also.
"There was nobody going to beat me on the night, especially in front of the crowd with my friends and family there."
McKillop, who has cerebral palsy, won the 800m in Beijing but was denied the chance to do the double because the longer distance was not on the programme in 2008.