Mothers took the drug while they were pregnant in the 1950s and 60s to treat their nausea. The drugs led to children being born with severe disabilities.
The president of the Michener Awards Foundation, Russell Mills, says the result of the Globe series was a promise by the federal government to provide fair compensation to the victims.
In March, the government announced survivors would get a lump sum payment of $125,000 and it also promised a $168-million fund would be set up to cover ongoing medical assistance.
Five other media outlets were honoured at the ceremony including The Canadian Press, which was given a Citation of Merit for its coverage of the federal Conservative government's overhaul of election laws.
The Michener Awards Foundation says The Canadian Press stories on the proposed legislation discovered the new bill would give a significant advantage to the governing Conservatives at the expense of their opponents.
Citations of merit were also given to the CBC, CBC North, the Vancouver Sun and L'actualite.
The CBC was recognized for its reporting on the temporary foreign workers program, which it revealed had become an easy way for employers to find foreign workers to fill low-skilled minimum wage jobs.
CBC North was honoured for its reporting on the death of an infant in Nunavut, which it used to highlight the specific health-care challenges facing Canada's northern communities.
The Vancouver Sun received the citation for its series "From Care to Where?" which documented the plight of foster children when they turn 19 and leave the care of the province of British Columbia.
L’actualité was similarly honoured for its eight-month investigation into how the military handles complaints of sexual assault and harassment. The series caused the chief of defence to announce an independent investigation.
The awards were handed out Thursday evening at Rideau Hall by Gov. Gen. David Johnston.