"You do great things," Benjamin Netanyahu told the University of Southern California professor in a call to his Los Angeles home.
"It's extraordinarily impressive, we are proud of you," a statement from Netanyahu's office quoted him as saying.
Later, Warshel told a press conference at USC that Netanyahu asked for a brief summary of his work, but warned the Nobel laureate he may not understand it.
"So I gave him a one-minute lecture. He understood it, and he said that from now on he will force his ministers to say whatever they want just in one minute," Warshel said as the room erupted with laughter.
Warshel, born in 1940 on a kibbutz in northern Israel, has been at USC since 1976 but told Israeli army radio he still feels connected to his roots.
"Part of me is Israeli," he said. "I visit the country, my daughters speak Hebrew."
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He said that it was 2:00 am in Los Angeles when he received the call from Stockholm telling him that he had won the prize with Martin Karplus, a US-Austrian citizen and Michael Levitt, a US-British citizen.
"They didn't have to say anything, the moment the phone rang I knew," he said.
"It was a very good feeling, because it wasn't certain," he added. "I expected it but it's never certain. Not certain if or when."
The three were honoured "for the development of multiscale models for complex chemical systems," the Nobel jury said.
The three were being recognised for "taking the experiment to cyberspace," it added.
Chemists all over the world simulate complex experiments on their computers thanks to work by the three that dates back to the 1970s, the Royal Swedish Academy of Sciences said in a statement.
The tool is "universal", helping pharmaceutical engineers to design new drugs or engineers to make cleaner energy sources or smarter manufactured products.
Warshel told the radio that he first thought of the ideas that led to the breakthrough in 1962 when he was still a student in Israel but did not know how to put them into practice.
"What earned the prize was something that was done in 1976," he said, the year in which he moved to the United States.