Sadiq Rilwan opened the scoring in the 32nd minute. Fantami Yusuf added the second in the 76th minute.
The result leaves the Savannah Tigers top of the table with nine points, five goals scored and none conceded. Enyimba remain without a point after two league matches.
Doma United had already beaten fellow newcomers Sporting Lagos 2-0 on the opening day and Inter Lagos 1-0 away. Saturday’s win against one of Nigeria’s most decorated clubs confirmed their status as early pace-setters.
The People’s Elephant struggled to break down a compact home defence and rarely threatened after falling behind. Doma stayed organised after the break and sealed the points when Yusuf finished in the 76th minute.
The NPFL had billed the fixture as one of the standout games of Matchday 3. Doma United now travel to Kano Pillars on 20 September.