The podium positions looked to be cemented with 200 metres to go, Van Vleuten's fatigue following the ten day Giro Rosa - which finished on Sunday - marked as her head thrashed almost in time with her legs over the finishing stretch.
However, as the line grew closer the Mithelton-Scott rider pushed a heavy gear to draw level and then pass her comparatively fresh legged Dutch compatriot.
Ashleigh Moolman-Pasio (Cervelo-Bigla) rolled in third, after her team mate Cecilie Uttrup Ludwig (Cervelo-Bigla) worked as a carrot for a three rider break to chase over the final climb of the race.
The 112.5 kilometres route from Annecy to Le Grand-Bornand comprised of very little flat land. Riders were treated to four classified climbs, including the cat 1 ascents of Col de la Romme and Col de la Colombiére - before a 13 km descent which gave way to a 1.5km finish stretch.
Organisers, ASO, opted to place the women's race on the day of the men's stage 10 - which just so happened to fall only one day after the final of the Giro Rosa.
The consecutive races both feature in the Women's World Tour calendar - so the most prolific members of the women's peloton were at both, and thus the tactics and dynamics of the day were massively influenced by the 10-days of racing in the legs of a large proportion of the field.
How it happened
Cracks appeared before the peloton arrived at the bottom of the first classified climb. However, it was following the cat four climb, the Col de Bluffy, when a strong group of three managed to gain a decisive gap on the peloton.
The first key break of the day was instigated by Leah Kirchmann (Sunweb), who was eventually joined by Lotta Lepistö (Cervelo-Bigla), Leah Thomas (UHC Pro Cycling), Małgorzata Jasińska (Movistar) and Anna Christian (Trek Drops).
Come 60km to go, the break's advantage had extended to 1-15, though in the peloton a number of attacks made building an advantage tough work - including one from Shara Gillow (FDJ Nouvelle-Aquitaine Futuroscope).
With 55km to go, on the descent of the Côte de Saint-Jean-de-Sixt, Christian dropped from the break; and at 45km remaining the quartet had 2-20 over the peloton, and 1-15 over Gillow and Christian, who were floating in the no-man's land between the two.
At the arrival of the Col de la Romme, Christian and Gillow had dropped back, leaving only the quartet out front to enliven the race.
As the slopes of the 9km climb - with its average gradient of 9 per cent - began to bite, Lepistö fell off the pace, followed by Jasinka, and finally Kirchmann - leaving only Thomas to go solo.
The next rider to attack from the peloton was Uttrup - leaving team mate Moolman-Pasio, who was second overall at the Giro Rosa - to nestle safely into the midst of the peloton.
Uttrup rode her way through the disintegrated break, to reach front player Thomas with 30km left - by which point she had 26s on the peloton, which largely consisted of team leaders aiming squarely at the win, with many domestiques dropped.
The Danish rider crested the climb with around 30s on the peloton, and with 35km to go, she had increased her lead on the descent - stretching the gap to 1-26.
On the descent, Lucinda Brand (Sunweb) - who was forth overall at the Giro Rosa - showed her negotiations with hairpins were markedly better than those of many who had climbed their way to the front of the bunch.
She passed Thomas with 22km remaining, making her the second rider on the road behind Uttrup. Brand was third in the Giro Rosa's mountain time trial - so represented a clear threat as the slopes of the Col de la Colombiére approached.
With 20km left, Mavi García (Movistar) attacked the peloton - giving way to a counter from Anna van der Breggen (Boels Dolmans) - with La Course's defending champion Annemiek van Vleuten (Mitchelton-Scott) and Moolman-Pasio on her wheel.
Uttrup's gap had sunk to 55s with 19km left, whilst Van der Breggen, Van Vleuten and Moolman-Pasio caught Brand with 18km remaining. The group was momentarily an out-front quartet - before the attack came and Brand was left to pedal her way to the top alone.
With 16km left, Van Vleuten put in a number of soft attacks, Moolman-Pasio free to leave Van der Breggen to close the gaps as Uttrup continued her solo plight, 17s up the road.
Once Van der Breggen made contact with Uttrup, Moolman-Pasio attacked immediately. However, a counter from Van der Breggen looked like it cost her very little effort to distance the other two. The only one of the trio not to ride the Giro looked significantly more comfortable than her companions.
Cresting the climb and on to the descent, Van der Breggen had clear road between her and the duo of Moolman-Pasio and Van Vleuten.
As the road tipped down, with 5km left Van der Breggen was 10s ahead of Van Vleuten and a good 45s ahead of Moolman-Pasio, who was being closed down by Brand, and behind her the remainder of the peloton.
With 3km left, world time trial champion Van Vleuten was, contrary to all likelihood, closing the gap - 7s between her and the fresh legs of Van der Breggen, down to 5s with 1.5km remaining as the road flattened out.
In the last 100 metres - it looked clear than Van Vleuten would never be able to catch those fresh legs. However, defying all expectation, at 50 metres she was level with and then passing her competitor.
The Giro Rosa winner pipped her competitor on the line, winning by a margin of 1s, whilst Moolman-Pasio rolled in third.
La Course 2018, Annecy to Le Grand-Bornand (112.5km)
1 Annemiek van Vlueten (Ned) Mitchelton-Scott, in 3-20-43
2 Anna van der Breggen (Ned) Boels-Dolmans at 1s
3 Ashleigh Moolman Pasio (RSA) Cervelo-Bigla, at 1-22
4 Cecilie Uttrup Ludwig (Den) Cervelo-Bigla, at 1-58
5 Megan Guarnier (USA) Boels-Dolmans, at 2-19
6 Katarzyna Niewiadoma (Pol) Canyon-SRAM, same time
7 Katie Hall (USA) United Healthcare, at 2-22
8 Amanda Spratt (Aus) Mitchelton-Scott, at same time
9 Ane Santesteban (Spa) Ale Cipollini, at 2-24
10 Erica Magnaldi (Ita) BePink, at same time
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