The best actor award went to Javier Nunez Florian, who disappeared with his co-star Analin de la Rua de la Torre, en route to the festival. Their movie, Una Noche, is about three Cuban teenagers who defect to the US.
London-born Lucy Molloy won best new director for the film, while African drama War Witch was named best narrative feature.
Its star, Rachel Mwanza, won the best actress prize, for her role as a girl who is abducted and forced to become a child soldier.
The best documentary award was given to The World Before Her, which contrasts the participants in a Miss India beauty pageant and a fundamentalist Hindu girls camp.
Cuban actors Florian and de la Torre went missing at Miami airport during a stop-over on their way to the Tribeca Film Festival.
Their co-star Dariel Arrechada, made it to New York for the premiere last week, and shared the best actor award with Florian.
Jurors praised the pair for “potent individual performances that together are even greater than the sum of their parts.”
Molloy, whose film also picked up the best cinematography prize, said she wished the stars could have been there to share the glory.
Other awards given out on Thursday night included best screenplay for Argentinian film All In, a romantic comedy about a professional poker player.
Holocaust documentary The Flat won best editing, while The Revisionaries – which highlights the politicising of children’s text books in Texas – received a special mention from the jury.