Simone Inzaghi's side moved to nine points from four matches as the western league phase reached the halfway point, the club bouncing back from last week's loss to Qatar's Al-Shamal.
"It was a tough game, I thought they played very well," said Watkins. "There's a lot of good teams in this competition but I thought it was an important win and it's nice to get a couple of goals."
Watkins gave Al-Hilal the perfect start in the sixth minute when he capitalised on Kalidou Koulibaly's ball-winning challenge midway inside the Shabab Al-Ahli half that put the Emirati side in trouble.
The former Chelsea defender drove into the penalty area before laying off possession to Watkins and, after holding off the challenge of Nemanja Maksimovic, he steered his shot into the bottom corner.
Watkins doubled his side's lead in the first minute after the interval when Yusuf Akcicek delivered an incisive pass from the halfway line and the England forward applied an expert finish.
The win means Al-Hilal pull level on points with Shabab Al-Ahli, who had won their opening three matches in the league phase.
The first eight finishers in the 16-team league phase in both east and west Asia progress to the next round while the quarter-finals, semi-finals and final will be played in a centralised format in Saudi Arabia in April and May.
