Members of the Giant-Shimano team of Marcel Kittel would be conspicuous by their absence in the closing stages and it emerged that Kittel, who won stages one, three and four, had a problem and would not contend the sprint. Greipel, of Lotto-Belisol, was the beneficiary; left out of position in the first three sprints of the Tour, the German champion finished arms aloft following a sixth Tour stage win of his career.
Alexander Kristoff (Katusha) was second and Samuel Dumoulin (Ag2r La Mondiale) third, while Vincenzo Nibali (Astana) finished safely in the pack to retain the race leader's yellow jersey which he claimed on stage two in Sheffield.
After the chaos of the cobbles on stage five - which forced defending champion Chris Froome to withdraw from the Tour - Team Sky's problems continued as Spaniard Xabier Zandio joined Froome on the sidelines having sustaining a suspected broken collarbone when he was caught up in a crash after 79km. It means that Richie Porte, who inherited the leadership of Team Sky from Froome, now has just six team-mates to call upon after less than a week of racing.
Egor Silin (Katusha) and Arnaud Demare (FDJ) also quit following the crash, while Jesus Hernandez (Tinkoff-Saxo), a key mountain domestique for Alberto Contador, abandoned soon afterwards. A temporary truce was then called between teams, with the peloton slowing to allow those riders embroiled in the crash but able to continue to rejoin the main bunch.
The accidents happened as the speed was increasing in preparation for the intermediate sprint. However, the crosswinds which the riders had been instructed to remain mindful of along the route did little to separate the peloton on a stage which always seemed likely to end in a bunch sprint. The day's four-man breakaway of Jerome Pineau (IAM), Thomas Leezer (Belkin), Luis Mate (Cofidis) and Arnaud Gerard (Bretagne-Seche Environnemen) led by around one minute 30 seconds with 65km to go. Pineau and Mate tried to prolong the breakaway, but their forlorn effort did not last.
The sprinters' teams were to the fore in the final 10km, with Omega Pharma-QuickStep working on the front for Mark Renshaw in the absence of Mark Cavendish. The finak 5km included nine roundabouts but the road was drying out after the wet start. Cannondale, Europcar and Katusha were prominent in the finale, with some interlopers, as Kittel dropped back with an apparent problem.
Michal Kwiatkowski (Omega Pharma-QuickStep) broke clear as the peloton came through the flamme rouge at 1km to go on the uphill finish and steal ahead, but he was swept up with 300m to go as the sprinters took over. Renshaw burst clear, but Greipel accelerated was still able to squeeze ahead to win the stage.
Having finished sixth at best in the previous sprints, Greipel seemed relieved and he will have an chance to add to maintain his success in today's 234.5km seventh stage from Epernay to Nancy, which is expected to end in a sprint.
"First of all it was a really nervous day," he said. "We had to stay all the time in front. At the end maybe it was not a lead-out train, but with all the roundabouts it was not possible. I had a good wheel with Mark Renshaw. With 250 metres to go I just said to myself I go full now. Whatever will happen will happen. It was not easy; we just said to ourselves we'll stay calm and go for it."
Porte, meanwhile, bemoaned the difficulties assailing his team. "It was such a stressful day; it was horrible actually. We lost Xabi Zandio to the crash, but the rest of us kept out of trouble and we're here to fight now."