The Croatian striker chose his moment well, tapping home in the 89th minute after a cross-shot was only parried by Seoul goalkeeper Yu Sang-hun.
Kis had only come off the bench with seven minutes remaining, and his intervention moved Seongnam to eight points from their opening four games, putting them third and just a point behind early leaders Jeonbuk Motors.
Pohang Steelers swept to a 4-1 win at Incheon United thanks to goals from Stanislav Iljutcenko, Ha Chang-rae, Lee Seung-mo and Song Min-kyu. Winless Incheon's reply came from Kim Ho-nam.
In just the second weekend of action as South Korea's domestic season returned amid the coronavirus pandemic it looked as though Jeonbuk were heading for a frustrating draw on Saturday.
But substitute Veldwijk outmuscled Yun Suk-young, whose slack defending was punished with a drilled, close-range finish from Han Kyo-won's cross in injury time.
In a frantic match, Hong Jeong-ho's glancing header from Son Jun-ho's free-kick had Jeonbuk in front and Cho Kyu-sung hit the post with the goal gaping, which would have doubled their lead before the break.
Busan were handed a lifeline in the second half when Lee Dong-jun was tripped by Kim Jin-su inside the box. It was difficult to decipher from television replays whether the full-back got a touch on the ball but referee Kim Hee-gon decided to stick with his original decision after a VAR check.
Romulo coolly rolled in the leveller from the penalty spot before Kim Byung-oh had a moment of woe when he missed a sitter shortly after as Busan found some momentum.
And Jeonbuk made it two wins from two to start their campaign thanks to Veldwijk's late intervention.
Daegu fell behind before earning a 1-1 draw at home to Pohang Steelers.
Aleksandar Palocevic timed his run well to slot home Song Min-kyu's cutback shortly before half-time for his second goal in as many weeks.
But Edgar Silva's powerful header midway through the second half earned a share of the spoils.
Sangju Sangmu are up and running for the campaign after a 2-0 triumph over Gangwon.
Kang Sang-woo's 22nd-minute penalty had the home side in front and Moon Seon-min's goal on the counter 12 minutes from time saw Sangmu make amends for a 4-0 loss at Ulsan last weekend.
Seoul finished third in the 2019 campaign and they took the lead at Gangwon, Park Dong-jin's deflected shot finding the net to put the visitors ahead at the break.
However, the hosts hit back in the second half, starting with substitute Kim Ji-hyun converting a cross to level. They then secured victory with two late goals, the first of them scored by Cho Jae-wan with a clever back-heeled finish.
Having created his side's second, Kim Seung-dae sealed the result less than a minute later, cutting inside onto his right foot to score with a low finish.
Meanwhile, Pohang Steelers were too strong for Busan I'Park, running out 2-0 winners.
Stanislav Iljutcenko opened the scoring midway through the first half but the home team were made to wait to seal the points, Serbia midfielder Aleksandar Palocevic eventually doubling their lead from the penalty spot in the 71st minute.
The K League season finally began on Friday - Jeonbuk Motors recording a 1-0 triumph over Suwon Bluewings - following a delay due to the coronavirus health crisis.
