Kopecky and van Vleuten had been the main aggressors of the day and that theme continued on the famous, steep final climb into Siena.
Van Vleuten's impressive surge saw all other riders distanced, and Kopecky herself hanging by a thread as they reached the top of the steepest sections of the paved ascent to the Piazza del Campo.
Kopecky was able to pass van Vleuten shortly after and it was a frantic battle from there, with positioning all important into the final right-hand hairpin, with just a short downhill run to the line to follow, meaning that the first through the corner would almost definitely win.
Both went into the corner hot with Kopecky holding her inside line, forcing van Vleuten to the outside and giving the younger Belgian rider the lead and the win in the Italian classic race.
"I mean, I cannot believe this but this was actually the plan for the team," Kopecky said. "Racing like this, with SD Worx is really super nice to do because I can attack myself, I have teammates behind me who have my back and I think today was perfect. I cannot believe this.
"You’re never confident [of beating van Vleuten] - we saw that last week - but I had a good feeling today and I knew the person to follow was Annemiek and first I had to let her go a bit.
"I don’t know what happened in my head but I just kept going and when we turned to the right I passed her but then the other corner she passed me again and it was really just one sprint to the last corner. It is amazing to win this race."
Van Vleuten was eager to make it three wins at Strade Bianche, talking at the start about how organisers had said they would name a gravel section after a three-time winner. She ultimately came up just one per cent short by her reckoning, due to some stomach issues.
“We were both fighting to go first through that last corner, because you know that there’s no room to overtake after that and you win if you go first - and Kopecky won that battle,” van Vleuten said.
“It was such a big battle - for sure I’d have liked to drop her on the climbs, but she was just super strong.
"I also didn’t have the best day, struggled with some stomach problems, and maybe I missed that last extra one per cent to be able to drop her. She was super strong, as I said, and she was still with me after the last slope, so I had to go for the sprint, too - it was a big battle.”
Earlier in the race, it was Rebecca Koerner (Uno-X ProCycling) who was the first rider to attack in chilly conditions in the Tuscany region and she was joined by Emily Newsom (EF Education-TIBCO-SVB). The pair pushed out their lead before Newsom dropped Koerner and was solo off the front of the race with a lead of four minutes.
Newsom recovered just after the longest gravel section as the peloton upped the ante to capture her with 55 kilometres remaining.
From there, a number of softening-up attacks saw the peloton have to respond to potentially dangerous moves, with Australia's Grace Brown (FDJ Nouvelle Aquitaine Futuroscope) prominent in the attacks and at the front of the peloton chasing down others.
Kopecky was one of the animators of the race, part of SD-Worx's strategy to get riders up the road and force others to work as she attacked with 21 kilometres remaining. She was brought back into the fold a few kilometres later.
After a number of attacks went and were brought back, with the chasing peloton reduced to just the elite riders, van Vleuten unleashed a stunning surge on a steep gravel climb with 12.5 kilometres to go.
Kopecky was glued to her wheel while others fell off the pace, with Demi Vollering attempting an attack over the top of van Vleuten before blowing up midway up the steep ascent.
The pair summited the climb with a 10-second lead, and Kopecky even helped van Vleuten a bit in setting the pace, though ultimately the cooperation wasn't enough to see them hold off the chasers and a group of 12 formed at the front.
There were attacks and counters in the final kilometres but everyone knew that the race would come down to the final pitches of the 16 per cent sections of the climb to Piazza del Campo, with Brown leading the way into the final kilometre.
Again it was van Vleuten's increase in tempo from the front that made the difference in the race, but the plucky Kopecky was able to cling on, out-manoeuvre van Vleuten in the final run to the line, and take a famous victory.