A spokeswoman for Cameron's Downing Street Office said the leaders had "constructive discussions" on a number of subjects, with the focus on the UK-Indonesian trade and investment relationship.
President Yudhoyono is on a state visit to Britain, aimed at boosting ties between the nations.
On the second day of the visit, the two leaders and Liberia's President Ellen Johnson Sirleaf also chaired talks in London on global efforts to fight poverty.
The Downing Street spokeswoman says Prime Minister Cameron and President Yudhoyono have sealed a defence deal which will boost cooperation in "research and development, investment and production".
They also announced a US$12.1 billion deal for BP to develop liquid natural gas in Indonesia, and signed an agreement strengthening links between the two countries' universities.
Prime Minister Cameron's spokeswoman says while he had praised the President for "his leading role in Indonesia's transition from autocracy to a vibrant democracy", the pair had discussed the protection of human rights in regions such as Papua.
Dozens of demonstrators gathered at Downing Street on Wednesday to protest against alleged rights abuses by President Yudhoyono's government in the Papua region and East Timor.
The two leaders and Johnson Sirleaf had also earlier chaired a panel of politicians from 26 countries charged with developing an anti-poverty strategy after the Millennium Development Goals expire in 2015.
The eight goals, established in 2000, set targets on improving education, health and women's rights, ending hunger, and protecting the environment.
Prime Minister Cameron says he believes world leaders now have a real opportunity to eradicate poverty.
"That is something politicians have been talking about for a while -- but for the first time I believe this generation really has the opportunity to do it," he said after the meeting.
"We think the Millennium Development Goals have made great progress.
" There's more progress to be made between now and 2015, but we're clear the next stage should be aiming to eradicate absolute poverty in our world completely."
The panel is meeting for three days in London, the second of four rounds of talks before it reports back to UN Secretary General Ban Ki-moon in May next year.
On Friday, the final day of Yudhoyono's state visit, he will address officials at the Foreign Office and meet with Indonesian business figures.
Queen Elizabeth II hosted a glittering banquet in honour of Yudhoyono and his wife Ani on Wednesday night, after formally welcoming them with a guard of honour and a ride in her ceremonial carriage.