"Welcome to the space station, Discovery. We're glad you're here," Mike Fincke the space station commander radioed to the shuttle's seven crew as the spacecraft docked.
He paid a special welcome to Wakata, who he described as the "first long-duration Japanese guy in space ever.''
Wakata replaces US astronaut Sally Magnus and will remain on board through May when the space station's crew is doubled from the current three to its full complement of six.
Discovery's crew are also due to intall special filter equipment to recycle astronaut's urine and condensation into fresh drinking water.
The new water system and the increased power delivered by the solar wings will be essential to service the station's expanded crew.
Over the next few days Wakata will begin work in the Kibo space laboratory – the Japanese-built module of the space station which was delivered last year.
|Discovery docked at the ISS two days after lifting off from Florida [EPA]
Kibo - meaning "hope" in Japanese – is the largest single module of the $100bn space station.
During his stay Wakata is expected to conduct a range of experiments in the lab, as well as some more off-beat challenges such as trying to fly on a carpet and use eyedrops in zero gravity.
The tasks are among 16 chosen from a list of more than 1,500 suggested by hundreds of Japanese residents, from nursery school pupils to a 90-year-old man, in response to a call from the Japanese space agency, Jaxa.
Wakata will try "a magic carpet that floats in the air", attempt to fold clothes, do push-ups and backflips, arm-wrestle another astronaut and "shoot liquid out of the straw of a drink container to see what happens", said the space agency.
Jaxa said it would release footage of the experiments to Japanese media.
In another initiative, the space agency has invited Japanese companies to rent an astronaut by the hour in the ISS space lab to perform desired tasks, which could include advertisements or science experiments.
The hourly charge for an astronaut is $55,000 plus an extra fee to transport any required items into space of $33,400 per kilogramme.