- Bats Right, Throws Right
- Height 6' 0", Weight 160-190 lb.
Phillips hit .191/.286/.206 as a backup infielder for the 2003 AZL Brewers in his only minor league season. He appeared for South Africa in the 2004 Olympics Africa-Oceania qualifier, which South Africa lost to the Australian national team. In the 2004 World Junior Championship, Phillips batted .267/.313/.267 for a South African team that batted a collective .104/.182/.120; Phillips had 4 errors in six games at shortstop. In 2005, Jonathan hit .383/.433/.533 for Heidenheim Heideköpfe in Bundesliga and fielded .925 at shortstop; he was not the first South African player to appear in Germany, following several others. Had he qualified, he would have ranked 7th in the division in average and 10th in slugging. In the 2005 Baseball World Cup, he batted .207/.233/.276 as South Africa's main third baseman. He was just 1 for 11 with two errors in the same role for the team in the 2006 World Baseball Classic.
In the 2008 Final Olympic Qualification Tournament, Phillips hit .273/.385/.409 to lead the offense and also played error-free ball at third base. His brother Anthony often played to his right as South Africa's shortstop. South Africa finished last and failed to advance to the Beijing Games.
During the 2009 World Baseball Classic, Phillips was 1 for 7 with a walk. His lone hit scored Martin Gordon with a run in the 9th inning against Cuba's Vladimir García. Hitting third in the 2009 Baseball World Cup, he was 1 for 8 with a run and a RBI; he played 1B in game 1 and CF the next two games. His lone hit came off Miguel Gonzalez of Cuba.
Back at third base for the 2013 World Baseball Classic Qualifiers, he hit .200/.429/.300 with a team-high three runs in three games. His four walks tied Karl Weitz for second on the team, behind Gift Ngoepe. In the 2017 World Baseball Classic Qualifiers, he played third and hit third for South Africa. He produced a .250/.444/.429 clip with four runs in four games. He tied Mitch Dening for second in the Sydney qualifier in runs, 3 behind his brother Anthony. He was also second to his brother in walks, 4 to 6.
With Ngoepe playing in the US and his brother coaching there early in 2019, Jonathan moved to short in the 2019 Africa Cup Baseball Championship, which South Africa won.