Borre opened the scoring on seven minutes from the penalty spot after he was brought down by Emmanuel Mas, while Fernandez tapped home a cross from Matias Suarez 20 minutes from time in Buenos Aires.
It was a repeat of last year's final, the second leg of which was played 10,000 kilometers away in Madrid -- and two weeks behind schedule -- after the original match was twice postponed.
It was a predictably frenetic start to a match that stirs such white hot passions in Argentine football.
River launched the first attack of note with Boca desperately scrambling the ball away as it pinged around the away box with players throwing themselves at it.
Play continued for about 90 seconds before referee Raphael Claus halted proceedings to consult VAR, where he spotted a clear foul by Mas on Borre.
Brazilian Claus was surrounded by the blue and yellow jerseys of Boca's incensed players and it was another couple of minutes before Borre could bury the spot-kick straight down the middle of Esteban Andrada's goal.
River fans at the 70,000 capacity Monumental were the ones denied the chance to watch the second leg of last year's final but they were now in full voice celebrating the opening goal.
The champions looked the more dangerous side but Boca's Alexis Mac Allister tested Franco Armani with a stunning long-range strike on 18 minutes that the Argentina goalkeeper had to tip over the bar.
Suarez and Borre forced saves from Andrada but Boca should have equalized on the counter attack two minutes before the break.
The burly Ramon Abila held off a defender to tee up Nicolas Capaldo, arriving at pace, just eight yards from goal but the midfielder spooned his left-foot effort high over the bar with only Armani to beat.
Uruguayan forward Nicolas De La Cruz almost made Boca pay before half-time but Andrada turned his curling, dipping, near-post free-kick over the bar.
Ten minutes into the second period, Boca coach Gustavo Alfaro introduced veteran former Manchester United and Manchester City forward Carlos Tevez.
As he ran onto the pitch, though, River almost extended their lead with Lucas Martinez slicing a cross from the right that sailed over Andrada only to clatter the post and bounce away to safety.
On the hour, a dangerous De La Cruz cross from the left pinged between two defenders and then off Andrada's head before sailing agonisingly wide of the far post.
River got the second goal they deserved as Fernandez played a one-two with Suarez before finishing smartly from six yards on 70 minutes.
In an entertaining end to the game, Armani tipped over Capaldo's curling effort from 20 yards while River substitute Ignacio Scocco headed wide.
To compound Boca's miserable night, deep into injury time Capaldo was sent off for a bad foul after another VAR review.
At least the match took place this time, after last year's humiliating circumstances.
Boca's players had refused to play the scheduled second leg at River's Monumental stadium after their team bus came under attack by home fans on its way to the ground.
Two Boca players required hospital treatment while others suffered effects from inhaling pepper spray fired by police to disperse River fans.
Boca appealed to South American football's governing body CONMEBOL and the Court of Arbitration for Sport to have the trophy awarded to them, but both bids failed and they were beaten 3-1 after extra-time in Madrid in December.
Brazilians Gremio and Flamengo meet in Wednesday's second semi-final.