He was born and grew up in Bloemfontein, where he attended Grey College and the University of the Free State. He is a qualified physiotherapist and worked for the Bloemfontein-based provincial rugby union team, the, in that capacity since 1997. When the Free State Cheetahs were formally included as part of the Super 12 franchise for the 1998 season, Nienaber also held the same role for them. In 2004, he also took over the role of Strength and Conditioning Coach at the Free State Cheetahs. He remained in that role when former South African national team flanker Rassie Erasmus took over as head coach in 2005, in a season that saw the team win the domestic Currie Cup trophy for only the second time in their history. The expansion of the Super 12 to 14 teams for the 2006 season saw the Cats effectively split into the and franchises and Nienaber was appointed the Strength and Conditioning Coach of the new Cheetahs franchise, where he again worked under head coach Erasmus. They helped the Cheetahs to a 10th and 11th-placed finish in 2006 and 2007 respectively, and also won the Currie Cup again with the Free State Cheetahs, sharing the title with the in 2006.
Nienaber moved to Cape Town to join Erasmus' staff when he was appointed Director of Rugby at Super Rugby franchise the and Currie Cup side prior to the 2008 season, moving into a role as a defence coach. After missing out on the play-offs in 2008 and 2009, an improvement in defence – which saw Western Province end the 2009 Currie Cup season with the fewest points conceded – also led to an improvement of the Stormers' fortunes. In 2010, the team finished second after the regular season, having conceded just 171 points in 13 matches, 117 points less than the, who had the second-best defence. The team made is all the way to the final, where they lost to fellow South African side the and Western Province achieved the same feat domestically, before losing to the in the 2010 Currie Cup final. Nienaber's record as a defence coach was noted by the South African national team, and was approached to join their staff, but the move was blocked by his existing employers. The Stormers again reached the play-offs in 2011 with the second best defensive record, and Western Province had the best defensive record in the 2011 Currie Cup. He was once again approached by the national team, and he was included in their coaching staff for the 2011 Rugby World Cup. South Africa had the best defensive record in the pool stage before losing 9–11 to in the quarter finals. He returned to domestic coaching with the Stormers and Western Province for 2012, as both teams again had the best defensive records in their respective competitions, with the Stormers reaching the semi-finals of the Super Rugby competition, while Nienaber tasted his first success with Western Province, as the team won the 2012 Currie Cup. Despite interest from other teams such as the, Nienaber remained with the Stormers and also joined the South African Rugby Union's newly formed Mobi-Unit, a coaching team headed up by Rassie Erasmus that would visit various teams at all levels of the game to impart coaching knowledge. The Stormers missed out on the 2013 Super Rugby play-offs despite having the best defensive record, while Western Province reached the 2013 Currie Cup final, which they lost to the Sharks. The Stormers endured a very poor season in 2014, finishing 11th, but Western Province won the 2014 Currie Cup final, their second during Nienaber's time at the team. At the end of 2014, they agreed to release him from his contract to join the SARU coaching staff on a full-time basis.
In April 2016, Rassie Erasmus was appointed as the Director of Rugby of Munster on a three-year contract, and Nienaber followed Erasmus, joining the Irish Pro12 side as a Defence Coach on a three-year contract.
