With the sides locked at 1-1 following the first leg of the quarter-final in Korea, a goalless draw at the Foolad Shahr Stadium would have been sufficient for the hosts to progress but Zob Ahan took the upper hand when Mohammad Ghazi volleyed home after 50 minutes.
But Yang Sang-min's header 14 minutes from the end sent the game into extra time and Suwon were gifted the winner when Mohammad Ahmadi pulled Stevica Ristic over in the box, collecting a second yellow card in the process.
Neretljak confidently smashed the spot kick into the bottom corner to send Suwon through 3-2 on aggregate.
A hard-fought first-half brought little in the way of clear-cut chances with both sides showing plenty of commitment in the middle of the park but lacking quality in the final third.
Zob Ahan had the first sight of goal in the ninth minute when Esmaeil Farhadi fired over from outside the box while Ghazi created an opening in the 26th minute when he drove at the visiting defence but sliced well wide from the edge of the area.
Suwon came close to taking the lead in bizarre circumstances three minutes before the break when a harmless-looking cross bounced over keeper Shahab Gordan and was heading into the net until defender Farshad Talebi acrobatically hooked it off the line.
Ghazi then spurned a great chance to put Zob Ahan in front in first-half stoppage time when Hugo Machado swung in a free-kick from the right but the forward glanced a free header the wrong side of the far post.
Ghazi made up for that miss five minutes into the second period, though, when he gave Zob Ahan the lead. Machado's flick-on was chested down by Igor Castro for Ghazi to volley first-time into the bottom corner from outside the box.
Suwon had a chance to reply two minutes later when Lee Sang-ho's pass released Oh Jang-eun but with Gordan charging out of his goal, the midfielder skewed his shot high and wide.
A slick build-up from Zob Ahan in the 67th minute ended with Castro back-heeling the ball into Hawar Mohammed's path but he steered a first-time shot well wide before Talebi saw a goal disallowed for offside.
Suwon then equalised with 16 minutes to go when Yeom Ki-hun dinked a ball towards the far post and Yang rose above the Zob Ahan defence to head home.
The Koreans should then have won the game five minutes from the end. Oh Beom-sok's penetrating run took him past two defenders and his low shot was parried into Lee's path but he fired over the top from inside the six-yard box as extra time ensued.
Zob Ahan then suffered a double setback seven minutes into the first additional period.
Ahmadi was booked for flattening Lee and from Yeom's resulting free-kick, pulled Ristic down in the box to concede a penalty and get himself sent-off. Neretljak stepped up and powered the spot-kick to Gordan's left and into the bottom corner.
Gordan turned Ristic's shot turned away at the near post as the interval approached while Ghazi latched onto a long ball three minutes into the second-half of extra time but shot straight at Suwon keeper Jung Sung-ryong.
Lee then tried to lob Gordan after he strayed from his box to clear but the Zob Ahan keeper recovered and Ristic raced clear with four minutes to go before lifting the ball over the onrushing Gordan but beyond the far post.