In the struggle for the overall leader's yellow jersey, Tadej Pogacar has a 3 minute 09 second advantage over defending champion Jonas Vingegaard, while Remco Evenepoel remains third at 5min 19sec with several potential game-changing stages still ahead.
The 24-year-old Evenepoel, on his first Tour de France, also holds a comfortable lead in the white jersey standings -- for the outstanding young rider.
But on this flat run in the south of France, last year's green jersey winner Philipsen emerged victorious and now has 344pts to the Eritrean Girmay's 376 in the sprint ranking.
Both men have three stage wins, but Philipsen lost crucial points in the green jersey tussle after being relegated from second to bottom spot for deviating from his line during the sixth stage in Dijon.
Leader Girmay fell at a roundabout less than 2 kilometres out in Nimes, with two Education First riders, and was unable to compete in the sprint for the line.
His elbow was bleeding but the usually smiling 24-year-old managed to remount and cruise home with a couple of team-mates, albeit ashen-faced.
"It's close, so we'll be playing it day by day now... You don't like to see anyone fall, I hope he can carry on," said Philipsen, who topped 70kph (43mph) as he raced over the line.
"Victories are hard to come by on the Tour de France so a third one is amazing," added the Belgian, who was led out by world champion Mathieu van der Poel.
Van der Poel is one of the favourites for the Olympic Games road race in Paris in two weeks' time.
Because of the Olympics, this year's Tour de France will finish in Nice on Sunday -- meaning there will be no final day dash down the iconic Champs Elysees.
Pogacar mentioned this after Tuesday's race.
"It's a shame for the sprinters not to have the final day sprint, they don't have that much motivation to finish the race but I hope they come all the way with us," said the yellow jersey holder.
The Tour de France race organisers extended the feared time cut on Sunday to allow Mark Cavendish and other haggard stragglers to remain on the race and compete in Tuesday's flat stage, where 152 survivors of the first 15 stages departed.
Cavendish won a record 35th stage win earlier in the Tour, but the veteran came 17th Tuesday.
Germany's Phil Bauhaus was second and Norway's Alexander Kristoff finished third.
Kristoff rides for Norwegian outfit Uno-X, two of whose team cars narrowly avoided a crash at a roundabout late in the race.
One of those cars had Johannes Kulset right behind it riding at 60kph.
This 16th day flat run was the last of the sprint stages with mountains galore on the menu from now on.
The race left the Gruissan salt basin with the mercury tipping 30 degrees Celsius (86 Fahrenheit) as the peloton rolled through the vineyards of the Aude region at speeds that fluctuated with the direction of the wind.
However, Wednesday's 17th stage takes the peloton back into the mountains with the finish line at a ski resort called SuperDevoluy.
The two killer climb stages then come on Friday and Saturday in the back country around Nice.
