The female panda Tian Tian came into season late on Wednesday night and she was artificially inseminated in the early hours of Thursday.
Keepers then tried to introduce her to male Yang Guang but her hormone levels had already dropped and he guessed she was not interested.
The zoo will now keep Tian Tian under observation for the three months in the hope that a panda cub will follow.
Edinburgh zoo acquired the pandas on loan from China in 2011 and previous attempts to mate the pair have failed.
Tian Tian, which means Sweetie, and male Yang Guang (Sunshine) were the first giant pandas to live in the UK for 17 years.
The last pandas in the UK, Ming Ming and Bao Bao, left a zoo in London in 1994 after failing to mate.

The 33-year-old world number one is this week ending her 14-year boycott of the BNP Paribas Open in California.
Her father accused fans of racial abuse after the then-19-year-old was booed and heckled in the 2001 final.
And speaking ahead of her return, the American top seed admitted: "I didn't think I would come back."
However, Williams, who last month confirmed she would play in the tournament in a Time magazine interview, said the time "felt right" to return.
The 19-time Grand Slam winner added: "There's not one thing that said I should come back, that I should come back in 2015. I didn't even know if I would be playing in this year.
"I just felt like it was the right time for me to come back here and try to be the best that I can be."
Williams beat Belgian Kim Clijsters in a final marred by the behaviour of some fans who heckled her and her family, apparently in response to sister Venus withdrawing injured from the semi-final between the siblings.
The watching Venus was also jeered by the crowd at the final.
"The whole point of me coming back was not to necessarily focus on what happened 14 years ago," Serena added.
Williams meets Romania's Monica Niculescu on Friday.
Edinburgh Zoo's pandas did not manage to mate naturally, it has emerged.
[NEXT_CONCEPT]
Serena Williams says she never believed she would return to Indian Wells after suffering crowd abuse at the tournament as a teenager.