The 69-year-old former secretary of state and the First lady, who was aiming to break the highest glass ceiling in the US by becoming the first woman president in the country's history, will give her concession speech later today, her aide said.
Clinton's call to Trump came after her Campaign Chairman John Podesta told her supporters gathered at an arena in New York for victory celebrations that they would wait till all the votes are counted.
"We are so proud of her. She's done an amazing job. And she is not done yet. So thank you for being with her. She has always been with you. I have to say this tonight. Good night. We will be back. We will have more to say. Let's get those votes counted and let's bring this home.
"Thank you so much for all that you've done," Podesta said in his brief remarks.
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There has been no official word from Clinton herself but her aide said she will deliver concession speech later today.
In his victory speech, Trump said he also congratulated Clinton and her family on a very, very hard-fought campaign.
"I mean, she fought very hard," he said. "Hillary has worked very long and very hard over a long period of time, and we owe her a major debt of gratitude for her service to our country. I mean that very sincerely.
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