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Uehara, who has coached the University team in the FootballSouth Premier League for the past four years, will coach Southern United in this summer's national league.
Southern United is the new name chosen for the Otago United side.
Uehara takes over from Richard Murray, who did not seek re-appointment when the job was advertised.
Uehara (43) was born in Brazil, and has a passion for coaching, having coached in both his homeland and Japan.
He has lived in New Zealand for more than a decade, after meeting his New Zealand wife Nicky overseas.
He is taking a long-term view of his new coaching position but believes there is the talent in the province to develop a good team.
''My philosophy is to have a multi-dimensional form of play. With that you need intelligent players who have the skills in terms of technique and can read the game both on and off the ball,'' he said.
''I see the young players we play against and play with in the premier league who are capable of doing this.
''Obviously, for this level of football results are very important, but primarily the focus is on performance and playing a good level of football.
''It is not going to be easy. It will be a challenge, especially being limited in terms of financial resources. But I know it is a cliche but I am a believer you try and get a group close together like a family and they work hard together so they can eventually overcome anything.''
It was going to take time for the side to get the results and the board was aware of that when it appointed him, he said.
He has signed an initial contract for one year with Southern United with an option for two more years. The position was paid but not a significant amount, he said.
The season kicks off in November and Uehara hopes to have his support team in place in the next couple of weeks.
''I think it is very important you have the right guys around you. You get the assistant coach, the fitness trainer.
''There is no magic formula. Look at the best teams in the word, Real Madrid, etc. They all have to work hard and it takes time to come together.''
Otago United has struggled in the past couple of years, finishing in the bottom reaches of the table, and competing against heavily resourced teams from Auckland.
Uehara, who is a football consultant for FootballSouth, is a teaching fellow with the School of Physical Education at the University of Otago.
He is completing a PhD in skill acquisition at the university and hopes to complete it next year.
Southern United chairman Phil Cunningham said Uehara's experience and approach won the board over. The organisation was looking forward to the season ahead and the impact the new coach would have.
Four people applied for the position.