Ambulances were called to aid around seven people who became nauseous while waiting in the Solna Centrum metro station, just north of central Stockholm, shortly before midnight on Wednesday night.
All trains to and from the station were halted and police also set up barricades around the building.
Those affected by the suspected mystery substance were given oxygen to cope with the effects of exposure to what some theorized was tear gas or pepper spray.
But neither police nor emergency crews were able to confirm what the substance may have been.
"And I don't think we'll ever figure it out," Anette Bäcklin of the Stockholm fire brigade told the TT news agency.
Firefighters with expertise in chemicals were called to the scene and examined the area with special equipment throughout the night and into Thursday morning.
But readings taken at the station's platforms, escalators, or ticket counters failed to produce any results or give clues as to what the nausea-inducing substance could have been.
Readings taken on people's clothes also proved fruitless.
However, the building was reopened and trains were once again operating normally by Thursday morning, despite the fact that investigators had failed to determine what may have caused people to become ill – including some firefighters who first arrived on the scene.
"They felt nauseous and their tongues went numb. But when they received oxygen, they felt better," said Åsa Dehlin of the Stockholm fire brigade to TT.