The undefeated "Monster" won by technical knockout in the seventh round at Ariake Arena when Doheny started hobbling and was unable to continue after injuring his hip.
The 31-year-old Inoue, who took his record to 28-0 with 25 wins by knockout, was making his second defence since becoming the undisputed super-bantamweight world champion last December.
Legendary American promoter Bob Arum said in an interview in the ring that Inoue would defend his titles once more in Tokyo in December before fighting in a "big celebration" in Las Vegas next year.
Inoue said nothing had been decided but he declined to rule out the possibility of a first bout in the United States since June 2021.
"This fight is just finished so I don't have anything to say," Inoue said when asked about Arum's comments.
"We also have talks about December and I'd like to speak to my promoter about that and decide."
Inoue is just the second man to become undisputed world champion at two different weights since the four-belt era began in 2004. American Terence Crawford was the first.
Inoue was fighting for the first time since he beat Mexico's Luis Nery in front of 55,000 fans at the Tokyo Dome in May.
Hip injury
That bout saw the Japanese fighter knocked down for the first time in his career but he never looked in serious danger against the 37-year-old Doheny on Tuesday.
Inoue had to be patient against his cautious opponent but he began to land some big body blows as the fight progressed.
The fight came to an abrupt halt when Doheny suddenly began limping about 20 seconds into the seventh round.
He was unable to walk and had to be helped from the ring by his team.
Doheny's trainer Hector Bermudez said his fighter had injured a sciatic nerve in the sixth round and "tried his best" to carry on.
"I know Inoue did a little flurry, a three-punch combination, but that wasn't what injured him," said Bermudez.
"He was already injured in the previous round."
Inoue was expected to dominate from the start but Doheny kept himself in the fight and made the champion work hard to find an opening.
Inoue said his plan had been to start the match cautiously and raise the pace around the sixth and seventh rounds.
He said his aim for the fight had been to "beat him with boxing".
"Maybe everyone was expecting the fight to turn out a little differently," he said.
"But personally, it's not something I'm worried about."
Doheny, who held the IBF super-bantamweight world title from 2018 to 2019, saw his record drop to 26-5, with 20 KOs.
On the undercard, Japan's Yoshiki Takei retained his WBO world bantamweight title with a unanimous decision win over countryman Daigo Higa.
Takei was making his first defence after taking the title from Australia's Jason Moloney in May.
