In a keenly contested pool B encounter, Muhammad Bhutta put Pakistan ahead in the third quarter before Nikkin Thimmaiah drew level at the start of the fourth.
Waqas took advantage of a defensive lapse to hit the winner that gave unbeaten Pakistan a place in the semi-finals even before their last league match against Oman on Saturday.
The winner between India and China on Saturday will determine the other semi-finalist from the pool. Both teams are level on six points from three matches. (Asian Games Hit by Hijab, Drugs Controversies)
Meanwhile, Kenta Tanaka and Toshiro Tachibana slammed hat-tricks as Japan blanked Singapore 13-0 to remain in contention for the semi-finals from pool A.
With two wins from three games, Japan drew level with hosts South Korea and Malaysia, who meet later on Wednesday after gaining full points from their first two matches.
Singapore ended the competition with four losses, having conceded 35 goals and scored only three.
Japan's Korean coach Kang Keon-Wook admitted Saturday's match against Malaysia will be crucial to his team's chances.
"Malaysia are a strong team so I guess it is going to be a pretty intense match," Kang said. "We have made plans for that game and ensure our strong points are not wasted."
Oman recorded their first win in three pool B games with a 3-1 romp over winless Sri Lanka, but the effort came too late to stay in line for the semi-finals.