Araba's attacker Abdiel Arroyo played a role in both goals, setting up the first and scoring the second as the Panamanians took all three points at W Connection's Hasely Crawford Stadium.
The victory on Thursday took Araba to six points from three games, lifting them to top of their group, two points clear of Major League Soccer's Houston Dynamo, who have a game in hand.
Araba edged ahead of W Connection just before the half-hour mark as left full-back Luis Fraiz burst down the wing, received a pass from Arroyo and thrashed the ball home for his maiden goal in the continental club competition.
The visitors completed their victory with 30 minutes remaining as Jose Gonzalez sent Arroyo in behind the home side's defence, and the 19-year-old winger rounded W Connection goalkeeper Alejandro Figueroa to score.
In the other clash on Thursday, Firpo of El Salvador defeated Victoria of Honduras 2-1.
Firpo moved up to four points in Group Seven, three behind leaders Tijuana of Mexico, while Victoria are bottom of the table and have yet to register a point.
