The duo broke away from the rest on the seventh lap on a dry, fast-paced course, exchanging blows before Orts faded in the final lap, allowing Nys to take his first major championship victory solo.
Eli Iserbyt (Belgium) was the best of the rest as he took the final place on the podium.
Nys made the final selection by accelerating when Iserbyt went in for a change of bike with two laps to go. Orts was able to go with him, but couldn't hold on to the young Belgian star as he set an infernal pace in the closing stages.
Orts had put in an heroic ride, roared on by the Spanish fans, but didn't have enough gas in the tank and was distanced in the final minute of racing.
Nys was delighted to win the European title, but found the course challenging from a tactical sense.
"It's a super difficult race because it's so fast and difficult to make a gap. So I went into the race with the feeling of just let it happen, you know, and try to adapt in every scenario," Nys said in the TV interview after the finish.
"I didn't expect to have so much control from the start. It was all clear in my head and I knew exactly what I had to do. The moment I took the front, I had full control over the race."
Nys, who turns 22 later this month, paid tribute to his companion at the front Felipe Orts, saying he was the "best guy" to have with him in the finale.
"He's super strong and I knew before coming here he would really be ready for this. I think it was really a big goal for him to be really good over here."
To have him with me is perfect because we understand each other really good. And we were both riding full for the podium spot. So it's perfect," he added.
How it unfolded
On Pontevedra's fast-paced course the start is crucial and it was Frenchman Rémi Lelandlais who launched off best of all to lead through the open stages of the race with almost the entire field in his wheel.
Towards the end of the first lap, Eli Iserbyt took the lead and to his fortune Lelandlais got tangled in the crowd barriers, gifting Iserbyt some clean air in front of his rivals. It was down to Lars van der Haar to chase down Iserbyt, who held a six second lead, the Dutchman looking strong as he reeled the Belgian in.
Pim Ronhaar lifted the pace and stretched the group on lap three, but although riders behind were struggling, the course made it difficult to break the group apart. Twenty riders were still in touch heading into the middle-section of the race.
The pace was on throughout and as the fifth lap began, riders started to drop off the back of the lead. Van der Haar kept things quick and the group splintered in several places without shattering completely. Home rider Felipe Orts responded by attacking into the most technical section to the delight of the home fans.
A group of three, Orts, Iserbyt and Nys gained a small gap after half-an-hour of racing, but it didn't seem decisive. Nys looked to stretch the deficit with Van der Haar leading the chasers less than ten seconds behind.
The trio ahead were working hard, but on the seventh lap Van der Haar attacked the chasers and bridged the gap, taking Niels Vandeputte with him to make a front group of five heading into the final two laps. Nys soon accelerated as Iserbyt went into the pits for a fresh bike, moving clear again with Orts and gaining a small gap. Again, Van der Haar took on the chasing.
The duo drew out their advantage on the penultimate lap and it looked as though the European championship would be fought for between Nys and Orts. Behind, Van der Haar, Iserbyt and Vandeputte would contend for the final place on the podium, twelve seconds down on the leaders heading into the final lap.
For the only time in the race, Orts refused to jump the planks on the final lap, carrying his bike over as the fatigue bit. Nys hopped over to gain a few crucial bike-lengths over the Spaniard. That gap grew over the following corners as Orts withered.
Nys stayed strong to take the first major championship victory of his career as Orts hung on for silver and Iserbyt broke away from Van der Haar and Vandeputte to take the final place on the podium.
