The return leg in Ethiopia will be played in a week.
Aguda clinically converted two second-half penalty kicks after Ajani Ibrahim went to the ground on 55 minutes and again on 84 minutes, when goal-bound Aguda was tripped from behind.
Bright Silas came close to adding another, but his effort came off the woodwork in the 72nd minute.
Rangers second half rally was a slight lift from their wasteful start as the crisp-passing game of the visitors endeared them to the fans.
Lobi Stars will be expected to overturn this result when both teams clash again in Makurdi in one week time.
Lobi Stars then chased the game thereafter with Alex Aghahowa failing to draw his team level late in the second half.
Striker Samad Kadiri could also have restored parity in stoppage time but somehow he failed to hit the target.