Malmström criticised a Thai court ruling that found Hall guilty of criminal defamation for alleging labour abuses at a firm supplying pineapples to Europe.
Last month, a Bangkok court handed Hall, of the Migrant Worker Rights Network, a three-year suspended sentence for defaming the Natural Fruit Company over a 2013 report that he helped write for Finland-based campaign group Finnwatch.
Malmström said the court ruling casts a "deep shadow" over recent labour rights reforms in the southeast Asian country.
Speaking on the Hall case, she said, "This verdict sends shivers through Thailand's already nervous human rights and social rights community. Criminal defamation laws are often used improperly by various actors to silence analysis and debate.
"Hall's reaction, that he was grateful for the international attention the case has brought to migrant rights in Thailand, testifies to his character in a way that the verdict does not because this is, of course, a much bigger question than one person."
She added, "We hope that the abuses and the type of abuses which Hall has documented will soon no longer be found in Thai factories.
"Respecting human rights is important, but it is also good business. Companies in Thailand and everywhere in the world who want to send to the EU need to understand that European consumers demand products free of labour abuse.
"I say to them that they should not underestimate the fundamental decency of the European consumer during her or his daily shopping. Do not underestimate the EU's - and the increasingly global - determination in ensuring decent work in global supply chains and more transparency.
"This is indeed an issue we are working on with companies to see if we can formulate a more coherent corporate social responsibility strategy that we are working on within the Commission.
"Hall, Finnwatch, Thai workers, migrant workers in Thailand and Thai officials working on labour rights all deserve our continued support and the closest possible cooperation to accelerate the process which is still so necessary."
Her comments come as the country enters a period of mourning over the death of Thailand's long serving monarch, King Bhumibol Adulyadej.
The monarch was also seen as a stabilising figure in a country often wracked by political turmoil.
Thailand remains under military rule following a coup in 2014.
Parliament last week passed a resolution which directed the EU to discuss this issue with the Thai government during a Commission delegation visit to the ASEAN-EU forum in Bangkok this week.
Hall told this website that the European Union should require companies to publicly disclose the origin of all products imported and sold within the 28-nation bloc to help stamp out labour abuses.
The data, he said, should be uploaded in a common database accessible by consumers, allowing them to make informed decisions on what they buy.
He urged EU lawmakers to follow the US' efforts to enhance transparency in the supply chain.
His call is supported by Heidi Hautala, an MEP with the Greens/European Free Alliance group, who said she was working to bring the idea to Parliament.
"It could be a very powerful tool for sustainability of supply chains," she said.