Detectives arrested a 20-year-old man before executing a search warrant at a home in Melbourne's west on Wednesday, where they seized multiple items.
The man has been charged with theft of a motor vehicle, along with failing to provide access to applications on his phone.
Police allege the man stole a blue 2020-model VW Golf sedan at Melton on November 29, 2024.
The stolen car was used in other offences, including the Lux nightclub arson at South Yarra in November, as well as an arson and shooting at Bundoora.
Investigators do not consider the Bundoora and South Yarra incidents politically motivated attacks.
Police believe the car was used in the Adass Israel Synagogue arson attack on December 6.
Two of the synagogue's three buildings in Ripponlea, in Melbourne's southeast, were gutted in the fire.
Inside at the time were two congregants preparing for morning prayers who escaped, with one suffering minor injuries.
Photos and CCTV footage released by counter-terror police in May showed a Golf sedan repeatedly passing the synagogue before parking directly outside its main entrance.
Three people donning hoodies and masks get out of the vehicle and use an axe to damage the entrance of the building.
No one has been charged with carrying out the firebombing and the accused car thief is the first person to be accused of any offence linked to the attack.
Terrorism investigators continue to investigate the attack as a priority.
Investigators have combed through CCTV from more than 1400 locations and believe multiple offenders are directly and indirectly linked to the synagogue arson, police confirmed in May.
Detectives have been investigating several alleged acts of anti-Semitism across Melbourne in July, including an incident at the Israeli restaurant Miznon and the alleged arson attack on a East Melbourne Synagogue on July 5.
A group of worshippers was forced to flee the synagogue when a man allegedly set the building on fire during weekly services.
Police have since charged a 34-year-old man with multiple offences including reckless conduct endangering life and criminal damage by fire.
Israeli Prime Minister Benjamin Netanyahu condemned the "reprehensible anti-Semitic attacks" on both the Melbourne synagogue and the restaurant.
Police are continuing to work with people from the synagogue and other representatives from the Jewish community to ensure they have appropriate supports.
The 20-year-old charged with car theft was granted strict conditional bail to appear at Melbourne Magistrates' Court on October 3.
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