Aberdein comes from a motorsport family; his father Chris Aberdein was an Audi works driver in South Africa during the 1990s. Jonathan began his single-seater career in 2016 and showed rapid development across multiple disciplines in a relatively short professional career.
Aberdein entered the 2016 ADAC Formula 4 Championship with Motopark as his first serious single-seater programme. He followed this immediately with the 2016–17 Formula 4 UAE Championship, where he was dominant: he won 14 of 18 races to claim the inaugural title of the series. Despite this dominance in the UAE, he could only manage ninth overall in the 2017 ADAC Formula 4 Championship, though he did record four podium finishes.
In 2018, still with Motopark following an extensive winter testing programme, Aberdein stepped up to the FIA Formula 3 European Championship. He took three podiums across the season—two at Silverstone and one at the Red Bull Ring—and finished twelfth in the championship standings.
Aberdein first sampled the DTM environment through a rookie test for Audi at the Lausitzring in 2017, followed by another Audi customer team test at Jerez in December 2018. These evaluations led to a full DTM season in 2019 with Audi Sport Team WRT. He finished tenth overall with 67 points, posting a best race result of fourth at both Assen and the Nürburgring.
His 2020 DTM season took a different route. Originally lined up as Audi's reserve driver across DTM and Formula E—a role that would have included a single race appearance replacing Robin Frijns at the Norisring—he instead joined BMW Team RMR for a full sophomore campaign. He matched his previous best result with a fourth place at Zolder and finished eleventh in the standings.
The move to prototype endurance racing in 2021 proved to be Aberdein's most fruitful chapter. Joining United Autosports in the European Le Mans Series alongside Tom Gamble and Philip Hanson, the trio accumulated four podiums including a victory at the season-ending round in Portugal to finish second in the LMP2 standings. That same year he also entered the 24 Hours of Le Mans with United alongside Nico Jamin and Manuel Maldonado, though a crash caused by Maldonado with the sister United car resulted in retirement.
For 2022, Aberdein joined Jota Sport in the FIA World Endurance Championship, partnering Ed Jones and Oliver Rasmussen. After mixed results at Sebring and a retirement at Spa-Francorchamps, the car recovered at Le Mans: the trio finished third in the LMP2 class at the 24 Hours, sharing the podium with the sister Jota entry that took overall LMP2 victory. They repeated with another third place at Fuji, ending the season sixth in the teams' standings.
Aberdein also made a brief return to GT racing in 2022, contesting the first two rounds of the ADAC GT Masters for Mercedes-AMG-affiliated Mann-Filter Team Landgraf and taking three podiums in the first three races. He additionally competed in the opening round of the 2022 Nürburgring Langstrecken-Serie with Team Sorg Rennsport, finishing eighth in the VT2 FWD class.
In 2023, Aberdein returned to the European Le Mans Series for Inter Europol Competition, driving the No. 43 LMP2 entry alongside Olli Caldwell and Rui Andrade. One podium at Paul Ricard was offset by three retirements from six races, leaving the team seventh in the standings. That 2023 season proved to be his most recent racing campaign.
Aberdein's career illustrates the modern pathway from formula car racing through touring cars and into endurance prototypes—a route taken by many drivers who find their strongest form in GT and LMP competition rather than single-seaters. His podium at Le Mans in 2022 and his runner-up finish in the 2021 ELMS LMP2 class represent the high-water marks of a career defined by consistent competitiveness across several disciplines.