The big German took advantage of Cav's premature surge to use the slipstream well and hold off a fast charging Peter Sagan by a hair's breadth on the line as Chris Froome and Alberto Contador took time out of Vincenzo Nibali and Nairo Quintana in the GC quest.
Fabian Cancellara, who beat Cavendish into fourth on the line, took the yellow jersey from Australia’s Rohan Dennis.
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Sadly for the green jersey contenders, breakaway riders took the big points at the first intermediate sprint, with the Czech Jan Barta scooping a maximum 20.
It was left to German John Degenkolb to pip his rivals to fifth place and 11 points with birthday boy Alexander Kristoff, Sagan and Cavendish taking 10, nine and eight points respectively in the battle for the green jersey.
Just after the sprint, we had our first crash of the race as Team Sky's Geraint Thomas and several others hit the tarmac. Thankfully for the British outfit and the rest, they all managed to get back in the saddle and make it back to the peloton.
Just when it looked like the stage would continue on a predictable course, the weather went ballistic and completely blew the peloton apart over a series of tricky roundabouts. The breakaway group were caught with Froome and Contador putting the hammer down on their yellow jersey rivals Quintana and Nibali.
Italian Nibali was having a particularly poor time of it as he picked up a puncture with just under 25km left. The Astana rider then used questionable tactics in an effort to get back in the swing of things behind a car on the road.
Sagan was the next to hit trouble with a wheel replacement hurting his chances of an opening stage win, a few Movistar riders then sliding off the tarmac at one of a plethora of roundabouts that also saw Joaquim Rodriguez hit problems.
The rain relented towards the finish, which allowed the sprinters in the leading bunch to work out their tactics ahead of time as Cav and Greipel eyed each other up for the finishing dash that culminated in the German taking the win leaving Sagan second and Swiss Fabian Cancellara third.
Lotto-Soudal's Greg Henderson summed up the feeling for the winning team: "Unbelievable. There was an ideal situation then a plan B, then a plan C. Greipel was so strong. We had all the elements thrown at us today and it is awesome. It was those roundabouts that split it. I am so happy."
Cancellara's cheeky third saw him take over the yellow jersey from Rohan Dennis with Tony Martin second and Tom Dumoulin third six seconds back. Yellow jersey outsider Tejay van Garderen is eighth 44 seconds behind Cancellara with Froome a further four seconds, Contador one minute off the pace and Nibali two minutes and nine seconds behind already.

Fabian Cancellara dons the yellow jersey

Image credit: Reuters

Hard to split Chris Froome and Alberto Contador here. After both crashed out of last year's race to hand Nibali a relatively easy passage to his first Tour de France victory, the duo worked together to crush the Italian and Colombian Quintana way before the mountains come into play.
Nibali's horror show will be hard to come back from mentally out of the two, Quintana's mountain skills arguably more potent. BMC Racing's Van Garderen also prospered from getting in the lead group and he could finally deliver on the promise that he showed early on in his pro career.

(l-r) Rohan Dennis, Chris Froome, Tom Dumoulin, Tony Martin line up at the start of stage 3

Image credit: Reuters

Vincenzo Nibali. The Italian was all over the place once that lead group got a jump on him. The puncture with 25km left hurt him bad, so credit for getting back on and battling back (albeit in controversial circumstances) however he is a hefty one minute and 21 seconds behind Froome in the overall standings now.
Monday's Stage 3 sees the riders start out in Anvers with a pretty easy 30km or so before the gradual inclines start leading into a Category Four at Cote de Bohissau.
The day's intermediate sprint will be tackled at Havelange on the highest point of the course with three further climbs rounding off what should be a more pedestrian day. Well, we said that today and look what happened so tune in tomorrow and see the field go at it once again.
Nibali suffered more than most in the crazy weather and this summed it up well.
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