Just under 22 percent of the 2.4 million eligible voters in the capital cast a ballot in favour of keeping Tempelhof, one of the oldest passenger airports in Europe and a symbol of the embattled city's survival during the Cold War.
A quorum of 25 percent was necessary to pass the referendum, the first in the city's history.
Tempelhof's backers had launched a slick advertising campaign with vintage images of Allied pilots ferrying supplies into the airport in West Berlin after the Soviets tried to starve the city into submission in 1948-49.
But Berlin Mayor Klaus Wowereit and his left-leaning government warned that reversing a decade-old decision to mothball Tempelhof would jeopardize plans to open an expanded international airport outside the city limits in 2011.
"I can understand the feelings of people who disagree with closing the airport for emotional or historical reasons," Wowereit said after the final ballots were counted.
"I would now ask the proponents of its continued operation to respect the majority."
The conservative opposition, however, vowed to keep up the pressure on the Berlin government, pointing to a 60-percent majority among those who turned out at the polls in favour of Tempelhof.
Backers, who also included Chancellor Angela Merkel, had called for Tempelhof to be revamped as a dedicated niche airport for business travellers.
Those pushing for its closure say Tempelhof's location near the city centre is a nuisance for residents and a security risk due to low-flying planes in a heavily populated area.
They have suggested the creation of a cultural and media centre in its vast terminal and a park to replace its runways.
Tempelhof's passenger numbers have dwindled in recent years despite its prime location as more airlines pulled out ahead of the scheduled closure in October.
The busiest regional airport, Tegel on Berlin's northwest fringe, is also due to be shut down before the expanded Schoenefeld facility becomes the capital's sole airport in three years' time.
The referendum revealed an enduring east-west divide in the capital 19 years after the fall of the Berlin Wall.
A solid majority of voters in west Berlin cast ballots in favour of maintaining Tempelhof, which analysts attributed to the still vibrant memories of the airlift into the western sector.
Eastern voters appeared to have been left cold by the campaign, in part due to strong support for the expansion of the Schoenefeld airport southeast of the city.
Turnout for the referendum, which would not have been legally binding, was low at 36 percent with many Berliners opting to enjoy a warm spring day instead of heading to polling stations.
Tempelhof opened in 1926 and a vast terminal built a decade later ranks as the largest building in western Europe.
After Berlin was split into east and west following World War II, the Allies flew in hundreds of thousands of tonnes of food, coal and other supplies, mainly into Tempelhof, in a virtually non-stop airlift when the Soviets blockaded West Berlin in 1948.
Even after the blockade was lifted in 1949, shipments continued until September of that year to build up a surplus in case of a renewed attempt by Joseph Stalin to cut off the west.