Fernandez, 60, a center-left Peronist and former cabinet chief, won 47.21% of the vote compared to center-right President Mauricio Macri's 41.42%, with more than 65% of the vote counted, the interior minister said.
The initial results indicated Fernandez could win the election outright without the need for a second round.
Fernandez thumped Macri in an August primary election with what was widely viewed as an unassailable 20-point lead over the president as an economic crisis gripped the country.