The poll follows a bitter campaign in which opposition leaders blamed Fernandez and the Dominican Liberation Party for recent price increases and for allegedly using government funds to buy support.
Fernandez, who was president from 1996 to 2000, was again elected in 2004.
The run-up to the poll was marred by violence in which three people, including a former congressman, were shot dead in a clash between supporters of Fernandez and Vargas on Wednesday in Villa Vasquez, about 200km northwest of the capital, Santo Domingo.
At least eight people, including two ruling party officials, also suffered gunshot wounds in clashes that took place on Thursday and Friday.
Fernandez, who helped pull the country out of an economic crisis triggered by the collapse of a leading bank in 2003, has vowed to introduce a "social pact" to address poverty and to increase government spending if he wins re-election.
However, he has faced criticism for spending hundreds of millions of dollars on building an underground transit system in Santo Domingo, a pet project aimed at easing congestion in the capital.
Voting for Dominican citizens abroad was also planned in 17 cities in Latin America, Europe and the US, including New York state, where Fernandez grew up.