One of them was a radar-equipped unit to complete a system of surveillance satellites that will allow Tokyo to monitor any place in the world at least once a day.
The other was a demonstration satellite to collect data for research and development.
The H-IIA rocket blasted off from the southern island of Tanegashima around 1:40 pm (0440 GMT) and released the satellites as planned, according to the Japan Aerospace Exploration Agency (JAXA).
"The rocket flew as planned and released both satellites," JAXA said in a statement, confirming its success.
From an altitude of several hundred kilometres, the radar satellite will be able to detect objects on the ground as small as a square metre, including at night and through cloud cover.
Prime Minister Shinzo Abe, who has taken a hardline stance on North Korea, hailed the successful launch.
"The government will make the most use out of the system... in order to enhance our country's national security and crisis management," he said in a statement, according to national broadcaster NHK.
Japan developed a plan to use several satellites as one group to gather intelligence in the late 1990s as a response to a long-range missile launch by Pyongyang in 1998.
The space agency has said the radar satellite would be used for information-gathering, including data following Japan's 2011 quake and tsunami, but did not mention North Korea by name.
But the launch came as Pyongyang has vowed to carry out more rocket launches and a third nuclear test in protest at tightened UN sanctions over its banned launches.
The North last year launched two long-range rockets.
The first failed in April but the second in December flew over the southern Okinawa island chain, jangling nerves in Japan.