The victory at the Seeb Sports Stadium was the fourth successive win for Suwaiq, who toppled Al Nasr at the top after the latter was held to a 1-1 draw by defending champion Dhofar in a Salalah derby.
For Suwaiq, two quick goals soon after the start of the second session was enough as national team players Ali al Busaidi and Abdulaziz al Miqbali found the target in the 49th and 58th minute respectively.
Mohammed al Siyabi reduced the margin in the 77th minute but Suwaiq hung on to emerge winner and lead the table with 12 points.
At the Al Saada Sports Complex, Younis al Mushaifri found the equaliser for Al Nasr in the 69th minute after Dhofar had surged ahead in the 52nd minute through Ahmed Saleem's goal. Al Nasr remained at second spot with ten points.
At the Sultan Qaboos Sports Complex, nine-time winner Fanja recorded its first win of the league with a 2-0 win over Al Arouba. Mohmmed al Najashi and Mohammed al Taki were the scorers for Fanja.
Saham's 3-0 win over Al Salam helped it climb to third spot with six points. Five teams have six points but Saham leads on goal-difference.
Muscat drew with Oman 1-1 to be at fourth place while Al Nahda's narrow 1-0 win over top-flight newcomer Mudhaibi kept it on sixth, a place behind Shabab.
Mirbat's 2-0 win over Sohar in an away game helped it remain among the five teams with six points.