Chan Siu Kwan put South China 1-0 up in the 10th minute after firing in the rebound when his initial shot was saved by goalkeeper Khairul Azhan Khalid.
Lo Kong Wai doubled South China's lead in the 53rd minute when he slotted the ball right between Khalid's legs.
South China continued to dominate and were rewarded with a third goal just three minutes later when winger Jack Sealy volleyed the ball home.
However, Pahang did get a consolation goal in the 62nd minute when Dickson Nwakeme found the back of the net with a volley of his own.
Despite winning the match 3-1, Gomez called on his side to maintain their focus as they will be facing Kitchee in the Hong Kong League Cup final on April 22.
"I know we are in the round of 16 but my mind is now with the League Cup final against Kitchee," Gomez told the South China Morning Post. "We had a good game and I am very happy that those players who do not play regularly also did a good job.
"We could have won by a bigger margin if we had taken our chances after going three goals up."