Fighting in the women's 57-kilogram division Monday, Matsumoto defeated Corina Caprioriu of Romania in the final, using her footwork to gain an advantage throughout the match.
Caprioriu was eventually disqualified during overtime for making an illegal attack from behind, but still got the silver medal.
The bronze medals were won by American Marti Malloy and Automne Pavia of France.
Japan had already won two silver medals and one bronze in judo, but it expects the gold virtually every time its athletes step on the mat.
Matsumoto said she talked to herself on the way to the final, telling herself to remain focused and calm.
"On behalf of my teammates, I am very happy that I was able to get a gold," Matsumoto said.
French President Francois Hollande watched from the stands as Pavia won a bronze for her country. Pavia said she was pleased he was in the arena to watch her compete.
"He said he was a little disappointed (that she didn't win gold) but was still very happy," she said.
Malloy's father, Marty, also watched his daughter win bronze from the stands, where he was wearing a T-shirt with "Malloy" emblazoned on it, designed like a judo uniform.
"All I can ever remember about my daughter is her going to judo tournaments since she was 6," he said.
Malloy wasn't sure how he would reward his daughter but said there would definitely be celebrations later.
"First I'm going to have a beer in her honour," he said.
In the men's 73K division, Mansur Isaev of Russia took gold over Riki Nakaya, the Japanese world champion and a favourite to win the division.
It was a close-fought final in which Isaev and Nakaya attempted to pin each other to the ground. Isaev was eventually able to throw Nakaya off balance before holding him down for the victory. After sitting on Nakaya's chest, Isaev got up, and held his arms out sideways in what appeared to be some showboating for the Russian fans.
It is Russia's second gold judo medal of the London Games. On Saturday, Arsen Galstyan won the country's first judo gold since the break-up of the Soviet Union.
Nakaya said he was disappointed not to have won another gold for Japan.
"I lost because my skills were not high enough," he said.
Isaev, 25, came seventh at the world championships last year. Earlier in the day, he also beat top-ranked Wang Ki-chun of South Korea in the semifinals. The bronze medals were won by Nyam-Ochir Sainjargal of Mongolia and Ugo Legrand of France.