Fernandez, who enjoyed a lethal attacking partnership with compatriot Santiago Silva for Banfield when they won the Apertura championship in December, beat goalkeeper Daniel Vega with a low shot after a brilliant lay-off by midfielder Walter Erviti.
"The result should have been bigger, I think," Banfield coach Julio Cesar Falcioni said after Vega, River's best player, made a string of fine saves.
"We won at a very difficult ground. It had been several years since Banfield last won here, so it's very good and motivating" he told reporters.
Silva, top scorer with 14 goals in the first half of the season, is no longer at Banfield, having returned to Velez Sarsfield following a year's loan.
Silva scored for Velez, winners of last year's Clausura in July, in their 1-1 draw at home to Colon on Saturday but missed a penalty when his side were leading.
On Saturday, Racing Club, who recruited well during the recess after a bitter fight against relegation, served notice of their intent to play a major role in the championship with a 3-0 home win over Rosario Central.
Diego Simeone's San Lorenzo won 1-0 away to Atletico Tucuman and his former Argentina team mate Juan Sebastian Veron inspired Estudiantes to a 3-0 victory over Arsenal on Friday.
