The 53-metre (174-foot) H-2A rocket, with the word Nippon - or Japan - painted on its side, blasted off and placed a satellite in orbit.
Launches were put on hold in November 2003, when controllers destroyed a rocket and its load of spy satellites after a booster failed to detach.
Correspondents say the space programme now faces stiff competition from China.
Space agency JAXA wants to revive the reputation of the H-2A, the centrepiece of the programme, and show that Japan remains a viable contender, they say.
The orange and white rocket roared up into a cloudy sky from the launch site, on the remote southern island of Tanegashima, at 1825 on Saturday (0925 GMT).
Around 40 minutes later it put a multi-purpose weather and navigation satellite into orbit.
Live TV showed scientists applauding and shaking hands in the control room.
The take-off had been delayed for two days by weather, and then for another hour because of a fault in the data transmission system.
The last rocket to be launched, in November 2003, was blown up in mid-air.
Its payload of two spy satellites intended to monitor North Korea were also destroyed.
Japan's embarrassment was compounded by the fact that China had put a man into space just weeks earlier, a feat which Tokyo has never attempted.