She said: "It was just overwhelming excitement, happiness mixed with sadness. He's always one to make us feel everything is OK. He said 'Don't worry about me, I'm OK.'"
During the conversation, Khadr said he had little hope of justice from the military commissions and said "he would try, if he can, not to attend the court," according to Elsamnah.
The chief military prosecutor for Guantanamo has prepared charges against Khadr that include murder, conspiracy, providing material support for terrorism and spying.
The charges, however, have not been formally filed and the US authorities may alter them as they did this month in the case of David Hicks, an Australian detainee.
No hearing has been scheduled for Khadr.
Elsamnah also said her son wants to rely only on the family's Canadian lawyer, Dennis Edney, and to fire his American lawyers.
She said: "He said that they haven't done anything for him. He wants to be tried as a Canadian, not as an American."
One of Khadr's US lawyers, Rick Wilson, said he shared his client's doubts about the fairness of the military trials and supported his bid for the Canadian lawyer to join his legal team.
Months of lobbying
The phone call was permitted after months of lobbying the military.
"He [Omar Khadr] said that they [American lawyers] haven't done anything for him, he wants to be tried as a Canadian, not as an American"
Maha Elsamnah, mother of Omar Khadr
Wilson, a law professor at American University in Washington, said: "We made arguments based on his youth and the amount of time he's spent away from his family, and apparently those were persuasive."
Elsamnah said a friend drove her from Toronto to Ottawa, where an official from Canada's foreign ministry helped co-ordinate the phone call. Khadr also spoke with his grandmother and his sister, she said.
Citing security concerns, the military rarely permits detainees at the isolated prison camp to contact their families by phone. A Guantanamo spokesman did not respond to a request for information about the call.
About 385 prisoners are held at Guantanamo on suspicion of links to al-Qaeda or the Taliban, including about 80 designated for release or transfer.
Khadr is one of three well-known detainees designated by the Pentagon to face criminal charges under new rules for military commissions. So far, only Hicks has been charged. A hearing is set for March 20 in his case.
The US supreme court on Monday denied a request filed on behalf of Khadr and the third detainee, Salim Ahmed Hamdan of Yemen, for quick review of their legal rights ahead of the tribunals, possibly as early as this summer.