Arnaud Démare (FDJ) took his first Tour de France victory on stage four of the 2017 race, in a finish which was blighted by crashes.
World champion Sagan was then disqualified for his involvement in Cavendish's crash, having initially been docked 30 seconds and 80 points by the race jury.
A relatively quiet day saw the final 10km ramp up in speed as the sprint teams began to setup their main men for victory.
But with all the fighting for position and some tricky corners in the closing 2km, there were two big incidents that saw riders hit the deck on the approach to the line.
The first crash came just before the flamme rouge and saw much of the middle of the peloton come down on the left hand side of the road, with race leader Geraint Thomas (Team Sky) getting caught up in the incident.
Green jersey Marcel Kittel (Quick-Step), who was hoping to take his second stage win of this Tour, was also caught up in the mayhem and was dropped as the sprinters at the front of the group continued on at a ferocious pace towards the line.
Those who avoided the first crash included Nacer Bouhanni (Cofidis), John Degenkolb (Trek-Segafredo), André Greipel (Lotto-Soudal) as well as Cavendish, Sagan, Kristoff and Démare among others.
But as everyone began to launch their sprint and move towards the right hand side of the road, Cavendish attempted to move around Sagan from the back of the group close to the barriers with 400m to go.
It appeared that the world champion caught Cavendish with his elbow as he edged to the right, sending the Manxman flying into the barriers and crashing to the ground.
That incident took down Degenkolb and Ben Swift (UAE Team Emirates) who both appeared to get back up shortly after. However, Cavendish remained on the ground and it looked likely he wouldn't be able to continue.
Ahead, Démare was able to weave his way through and power ahead as Kristoff began to fade. Sagan, who was involved in that incident shortly before, was still able to close up on the sprinters ahead but wasn't able to stop Démare, who took his first ever stage at the Tour ahead of Sagan.
Sagan was subsequently disqualified for his part in the Cavendish crash, meaning a new green jersey winner will be crowned this year.
Geraint Thomas, in spite of the crash, was able to safely finish and retain the overall lead while his team-mate Chris Froome also remained safe along with the other GC contenders.
Watch: Tour de France 2017 stage four highlights
A mega solo break
The day began quietly with another route of 200km on the cards ahead of the first summit finish on Wednesday's stage five.
From the drop of the flag, only one man, Guillaume Van Keirsbulck (Wanty-Groupe Gobert) was willing to get away into the breakaway, and was perhaps surprised by the lack of other riders wanting to join him.
With no movement behind, the Belgian then pushed on alone with still more than 200km to go on the flat, 207.5km route.
The peloton were happy let him get a huge chunk of time with complete confidence they'd bring him back.
Van Keirsbulck gained almost 13 minutes on the bunch, before things began to turn on him. The gap quickly tumbled with 60km to go, and the lone leader looked doomed.
He was eventually dragged back in with 16.8km to go, as the sprint teams really began to engage themselves towards the finish.
It was then that the carnage ensued within the final couple of kilometres after a lot of jostling between teams on the run-in to town.
But despite the controversy between Sagan and Cavendish, Démare emerged a deserving winner with enough power and sped that he didn't look like anyone would have beaten him to his maiden Tour win.
The Tour de France continues on Wednesday with stage five; a 160.5km to the first summit finish at Le Plance des Belles Filles.
Tour de France 2017, stage four: Mondotf-les-Bains - Vittel (207.5km)
1 Arnaud Demare (Fra) FDJ, in 4-53-54
2 Alexander Kristoff (Nor) Katusha-Alpecin
3 André Greipel (Ger) Lotto Soudal
4 Nacer Bouhanni (Fra) Cofidis, Solutions Credits
5 Adrien Petit (Fra) Direct Energie
6 Jurgen Roelandts (Bel) Lotto Soudal
7 Michael Matthews (Aus) Team Sunweb
8 Manuele Mori (Ita) UAE Team Emirates
9 Tiesj Benoot (Bel) Lotto Soudal
10 Zdenek Stybar (Cze) Quick-Step Floors, all same time
115 Peter Sagan (Svk) Bora-Hansgrohe, at 30s (penalty)
General classification after stage four
1 Geraint Thomas (GBr) Team Sky, in 14-54-25
2 Peter Sagan (Svk) Bora-Hansgrohe, at 7s
3 Christopher Froome (GBr) Team Sky, at 12s
4 Michael Matthews (Aus) Team Sunweb, at 12s
5 Edvald Boasson Hagen (Nor) Dimension Data, at 16s
6 Pierre Latour (Fra) AG2R La Mondialeat 25s
7 Philippe Gilbert (Bel) Quick-Step Floors, at 30s
8 Michal Kwiatkowski (Pol) Team Sky, at 32s
9 Tim Wellens (Bel) Lotto Soudal, at 32s
10 Arnaud Démare (Fra) FDJ, at 33s
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