Natalie, who plays mortal scientist Jane Foster, acts as Thor's love interest in the franchise, played by Chris.
After the main filming was finished, the stars were asked to reshoot one final "passionate" love scene which comes up after the credits.
"Chris was working in Hong Kong and I couldn't get there because I was working on my own film," Natalie told the New York Daily News.
"And so they put his wife in my wig and costume, that's why it was so passionate. It was such a perfect solution, wasn't it?" she added.
Chris Hemsworth and his wife Elsa Pataky
The kissing scene between Chris and his wife, actress and model Elsa Pataky, was pulled off neatly thanks to careful camera positioning that shows Elsa from the back.
The couple, who tied the knot in 2010, announced last month that they were expecting their second child together. Chris and Elsa are already parents to one-year-old daughter India Rose.
Natalie, meanwhile, married her Black Swan co-star Benjamin Millepied last year. The couple have a two-year-old son together, Aleph.