Field Marshal Mohammed Hussein Tantawi, who had worked closely the US army chiefs for decades, was ordered to go into retirement on Sunday.
The move came after weeks of tension between Mr Mursi and the military.
The Pentagon, a large aid donor to Eygpt's army, said it expected to maintain close ties with the military.
The generals had assumed presidential powers after the ousting of President Hosni Mubarak last year.
Although President Mursi's announcement startled observers, the BBC's Kim Ghattas in Washington says the US showed no sign of surprise.
As the US gives more than $1bn in aid to the Egyptian military, it would expect some degree of consultation or warning, she says.
The new Egyptian defence team is made of up officials who have trained in the US and are known to the Pentagon, our correspondent adds.
"We had expected President Mursi at some point to co-ordinate changes in the military leadership, to name a new team," Pentagon spokesman George Little told reporters.
"The United States and the Department of Defence in particular look forward to continuing a very close relationship with the Scaf (Supreme Council of the Armed Forces)."
Field Marshal Tantawi has been replaced as both armed forces chief and defence minister by head of military intelligence Abdul Fattah al-Sisi.
"The new defence minister is someone who is known to us, he comes from within the ranks of the Scaf and we believe we'll be able to continue the strong partnership that we have with Egypt," Mr Little said.
He added that US Defence Secretary Leon Panetta looked forward to calling the new secretary "at the earliest possible moment".
US state department spokeswoman Victoria Nuland also said it was important that Egypt's civilian leadership and the military worked together "to advance the goals of the democratic transition in Egypt".
Egypt has been a key US ally since the 1979 Israeli-Egyptian peace deal.
However, since the election of Islamist Mr Mursi as Egypt's first democratically elected president, there have been fears that he might try to renegotiate the treaty.
So far the Egyptian military has shown no sign of challenging Field Marshal Tantawi's replacement.
Correspondents say Egyptians will see the dismissals as a decisive move in a struggle for power between the country's newly elected politicians and the generals who have exercised power for many years.
Also on Sunday, Mr Mursi annulled a key constitutional declaration issued in June which gave the military legislative powers and budgetary controls as well as the right to oversee the process of drawing up a new permanent constitution.
It is not clear how the Supreme Constitutional Court will react to Mr Mursi's move to nullify the decree.
The military council has in the past appeared to be at odds with the Muslim Brotherhood which now dominates parliament with its Freedom and Justice Party (FJP).
Mr Mursi resigned from his leadership positions within the Brotherhood, including his role as chairman of the FJP, when he won the presidential election in June.
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