Alaphilippe and Mollema jumped out to a gap of 30 seconds inside the final eight kilometres of racing and the Frenchman was dominant in the final, flat sprint, with Mollema forced to settle for second. Anthony Roux (Groupama-FDJ) finished third 16 seconds behind.
Alaphilippe had come into the race as one of the favourites, but the Spanish classic has a history of throwing up less-fancied winners. The Frenchman showed that he wasn't feeling the effects of any post-Tour hangover, showing himself to be the strongest on the notorious final climb of the Murgil Tontorra.
"I want to say a big thank you to my teammates," said Alaphilippe, "who protected and helped me throughout the day, believing in my chances. I am very happy after this win, because San Sebastian is a special race which I like a lot and it means a lot to conclude this part of the season with another beautiful victory."
I knew that the race suited my characteristics, but I honestly didn’t expect to win today. I didn’t feel very good, as I was tired after a long and hard Tour de France, but stayed focused in the final and made my effort at the right time, using the last climb as launch pad."
The early moves were brought back by the combined efforts of Astana, BMC and Bahrain Merida. Trek-Segafredo had also done their share of the work in the early stages and it was team leader Mollema and his Trek teammates who took control on the final ascent of the race, the Murgil Tontorra. The relentless pace reduced the peloton to just a fraction of the race starters.
Antwan Tolhoek (LottoNL-Jumbo) was the first to jump, with Rudy Mollard (Groupama-FDJ) the only rider able to match the young Dutchman on the steeper pinches of the ascent.
Mollema made the move to bridge to the front pair and drop them, with only Alaphilippe able to respond from the peloton to join the Dutchman. The pair pushed out the gap and then maintained it in the run down into the finish, where Alaphilippe took the victory.
The race was overshadowed by a crash with just under 20 kilometres remaining. Egan Bernal (Team Sky) and Mikel Landa (Movistar) were taken to hospital.
An announcement from Movistar has confirmed a non-displaced vertebrae fracture for Landa, with his Vuelta participation still up in the air.
Tour de France revelation, Egan Bernal, suffered a nasal fracture and severe maxillary injury in the fall. He had surgery on his nose and mouth, tweeting afterwards that the surgery had been successful but he still had two teeth missing.