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.
Indian tennis players Yuki Bhambri,Sanam Singh and Ankita Raina registered comfortable wins in their respective singles matches to sail into the pre-quarterfinals on Thursday.
All the three Indians were hardly tested by their opponents as they registered straight set wins without breaking any sweat at the Yeorumul Tennis Courts.
The Indian men's compound archery team put on spirited show to beat Iran 231-227 in the semi-finals to enter the final. India will face hosts South Korea in the title clash.
The Indian trio of Abhishek Verma, Sandeep Kumar and Rajat Chauhan, managed a total of 15 10s and got a score of 231 from 24 shots.
The Iranian team, comprising Esmaeil Ebadi, Majid Gheidi and Amir Kazempour, had 14 10's for a total of 227. What hurt the Iranians was a poor seven in the second set and an eight in the penultimate shot.
Sawarn Singh gave the Indian rowing contingent their second Incheon Asian Games medal by winning the bronze in the men's singles sculls at the Chungju Tangeum Lake Rowing Center at Incheon on Thursday.
With a time of seven minutes and 10.65 seconds, Sawarn finished third in the 2,000 metre race behind Iran's Mohsen Shadinaghadeh and Kim Dongyong of South Korea, who took gold and silver respectively.
Dushiant Dushyant had clinched the bronze in the men's lightweight single sculls final Wednesday for India's first rowing medal in the 2014 Games.
Indian shuttler Parupalli Kashyap marched into the men's singles pre-quarterfinals with a facile straight-game win over Afghanistan Iqbal Ahmad Shekib in the 17th Asian Games at the Gyeyang Gymnasium here Thursday.
Kashyap, who received a bye in the opening round, beat his Afghani opponent 21-6, 21-6 in just 17 minutes to book a place in the next round.
Indian shooters were off to anunimpressive start on the sixth day with none of them managing a podium finish.
In the 50m Rifle Prone Men's Team Finals, India finished fourth behind behind Kazakhstan, South Korea and China, narrowly missing out on a medal after aggregating a total score of 1852.8 with the help of 97x at the Okryeon International Shooting Range.
In the individual event, Joydeep Karmakar finished 10th in qualification, Gagan Narang was placed 14th while Hariom Singh was way behind at 29th.
In 25m Standard Pistol Men's Team event, India finished fifth behind Vietnam, Singapore, South Korea and formidable China with a total score of 1684 that included 34x.
In the 25m standard pistol individual event, Gurpreet Singh was the best-placed India at fifth position, Mahaveer Singh was next at 17th while Samaresh Jung could manage only a 24th-place finish.