Lieutenant Colonel Benedict Tomkins, 49, of Defence, Equipment and Support, based at Abbey Wood, near Bristol, is facing trial in the US.
He allegedly attacked the woman in her hotel room where he went under false pretences after a drinks reception.
The woman told the court Mr Tomkins was "very aggressive" and "took control".
The trial is being heard at Joint Base Andrews in Maryland. It is the first-ever court martial which will be held in the US and UK to allow more witnesses to testify.
The court heard that Mr Tomkins said he had had sexual activity with the woman, which "wasn't rose petals or cupid's arrows, it was fairly animal".
The incident is alleged to have happened after a dinner and a drinks reception at the Sheraton Hotel, Kampala, on 7 January 2015.
By the end of the evening, the young woman said she was "very drunk" when Mr Tomkins went to her hotel room.
"There was no talking, no romantic lead up to something that I recall. He did get much more aggressive and used some level of force to take things further," she said.
"The room was spinning, it was a very brief memory."
They later exchanged messages and he thanked her for a "wonderful evening" to which she agreed. She told investigators she initially feared reporting the incident in case it would harm her career.
The case is expected to resume in Bulford, Wiltshire, on Monday.

26 July 2016 Last updated at 17:48 BST
The company says its Dtek50 smartphone offers improved security over rival Android devices, and will cost less than its previous handset Priv.
It is the firm's second Android handset after switching focus away from its struggling BB10 platform.
One analyst said the phone was the "right move" but that the company still faced an "uphill battle" with devices.

The parade also commemorates Yeovilton's 75th birthday and is in recognition of the 70th anniversary of the end of World War Two.
Platoons from HMS Heron, led by the Queen's Colours and the Band of the Royal Marines, marched before Yeovil mayor Mike Lock.
There was also a flypast representing all the squadrons based at Yeovilton.
Lieutenant Commander Chris Gray said the freedom of Yeovil was granted to the base in 1962 and the parade "reinforces our bond and close links" with the town.

She was discovered by soldiers investigating suspected members of Islamist militant group Boko Haram.
Nigeria's military said the young woman is undergoing medical checks.
A total of 276 schoolgirls were kidnapped by Boko Haram from the town of Chibok in April 2014. About 200 of them are still in captivity.
More than 20 were released in October in a deal brokered by the International Red Cross. Others have escaped or been rescued.
Over Christmas, 21 of the young women freed under the October deal returned home for the first time.
However, family members told the BBC that they were kept in a politician's house and barred from going to their family homes.
A statement from the office of state governor Kashim Shettima acknowledged that "armed soldiers... escorted the 21 girls to Chibok and remain their strict guards throughout Christmas".
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Prior to this, the girls had reportedly been held in a secret location for debriefing by the Nigerian government.
Two weeks ago, Nigeria's President Muhammadu Buhari said the army had driven Boko Haram's militants from the last camp in their Sambisa forest stronghold in north-eastern Nigeria.
"The terrorists are on the run and no longer have a place to hide," Mr Buhari said in a statement.
Boko Haram has killed 15,000 people and displaced over two million during its seven-year battle to create an Islamic caliphate in the north-east of the country.
A married British Army officer denies raping a young female colleague at a UN event in Uganda, a court martial has heard.
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Blackberry has launched its first touchscreen-only Android handset, in a bid to diversify its range of devices.
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Royal Marines from RNAS Yeovilton have marched through Yeovil to mark the base's freedom of the town.
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The Nigerian army says that one of the abducted Chibok schoolgirls has been found, along with her six-month-old baby.