CCTV captured what appeared to be three men driving through the front windows of the store in Altona Meadows about 11.55pm on Saturday night.
They then loaded their vehicle with a number of expensive bikes before driving off.
The car allegedly involved in the ram raid was spotted by police overnight with two men inside.
A 26-year-old Drysdale man and 50-year-old Footscray man were both arrested and taken into police custody after the incident.
The Drysdale man has been charged with three counts of ram raid burglary at bike shops in Williamstown, Box Hill and Carnegie this month.
He is also facing charges over cars stolen in West Footscray and Flemington, the burglary of a Tottenham bottle shop and committing an indictable offence while on bail.
The estimated worth of all the stolen items, including cars and bikes, is about $180,000.
The 26-year-old is expected to appear at the Melbourne Magistrates Court this evening, while the Footscray man was released pending enquiries.