Captain Kiconco Tabaro said: "This man has been in the bush for quiet long. He knows the tactics, he knows the methods, he knows the sources of weapons.
"He has been one of our most wanted commanders. Once he recovers, then we expect a lot from him."
Ugandan soldiers helped Kwoyelo out of an old cargo aircraft. He wore a faded military jacket, buttoned to cover his injuries.
Sitting later in an ambulance at a military airport 40km from the capital Kampala, Kwoyelo said the rebels had split into three groups but he did not know the fate of the leaders.
Describing his capture, Kwoyelo said: "We just bumped into [Uganda's army] somewhere, and that was it."
Assault on hideouts
Ugandan troops led an assault on LRA hideouts in mid-December but have failed to catch Joseph Kony, the group's elusive leader, or either of his two indicted deputies.
In reprisal for the offensive, the rebels have attacked villages in the DRC, massacring more than 900 people.
Kony's two-decade rebellion against the Ugandan government has killed tens of thousands of people, driven some two million from their homes and destabilised a large part of central Africa.
Last year, Kony refused to sign a peace deal reached after two years of talks in neighbouring south Sudan, prompting the military offensive.
Aid workers accuse Kampala, Kinshasa and UN peacekeepers in DRC of failing to protect civilians from LRA reprisals.
Kampala says an end-of-February deadline to withdraw its troops from Congolese soil has been extended but a Congolese minister has rejected that.