The defeat leaves River mired in a slump, having lost six of their last seven league matches as they sit sixth in Group B of the Clausura competition with 21 points, 10 adrift of leaders Rosario Central.
Boca, meanwhile, notched a third straight league win to move top of Group A with 26 points and secure an automatic place in next year’s Copa Libertadores group stage, climbing to 59 points in the overall season table.
A scrappy first half offered little in the way of clear scoring chances until Boca grabbed the lead in stoppage time when Zeballos capitalised on sloppy River defending, cutting inside to fire past goalkeeper Franco Armani at the second attempt.
Boca doubled their advantage two minutes into the second half when Zeballos burst down the left and cut the ball across for Merentiel, who tapped into an empty net.
The hosts took full control of the game, pressing for a third. Merentiel thought he had doubled his tally but his effort was disallowed for offside, and a late penalty initially earned by Milton Gimenez was overturned following a VAR review.
Boca will host Tigre on the final matchday of the competition next Sunday, while River will play at Velez.