The first vehicle to visit the pump was GM/Opel's HydroGen3 prototype with fuel-cell propulsion system.
The filling station is operated by the Swedish-based power supply enterprise, Sydkraft.
The environmentally-friendly fuel is produced directly on site from water using electrolysis, and the electric energy needed for this is generated with wind power.
Sydkraft Gas president Per Lindell said: 'We want to demonstrate here that hydrogen is a clean, renewable fuel.'
The Malmö facility has enough fuel to fill about 25 passenger car tanks a day. HydroGen3 is based on the Opel Zafira.
The benefits of hydrogen are that it can be produced relatively simply from water and can be stored. It is also completely non-polluting.