"It doesn't look to be anything serious, but I have some abrasions and pain, so the team will continue to monitor me overnight," Alaphilippe said in a statement released by the team.
"I really don't know what happened, just that it was a touch of wheels in front of me and in the next moment I was on the ground," he said. "It's the first time in my career that I crash at high speed, but at the end of the day I am happy I could finish the stage. The only thing that we can do now is see how things go and how I feel in the morning."
Alaphilippe and teammate Enric Mas were part of a crash near the end of the 191.4km stage from Sarriguren to Estibaliz that also involved Team Sky's Geraint Thomas, Michael Kwiatkowski and Jonathan Castroviejo, who was taken to hospital with a suspected broken collarbone.
Both Deceuninck-QuickStep riders finished the stage; Mas was able to remount quickly but ended up conceding 1:40 at the line, while Alaphlippe, who started the day second overall just five seconds down, was attended to by medical staff before getting on his bike and finishing the stage 12:12 behind winer Max Schachmann (Bora-Hansgrohe).
Alaphilippe is now 77th overall at 12:24, while Mas dropped from seventh to 34th, 2:21 behind overall leader Schachmann.
Deceuninck-Quick Step directeur sportif Klaas Lodewyck told Cyclingnews the team will wait until morning to see how Alaphilippe feels before deciding if he'll start stage 4, a 163.6km race from Vitoria-Gasteiz to Arrigorriaga.
"The main goal for us was to put him on the bike and get him at the finish line," Lodewyck said. "Now the doctor will look into it or what could be wrong and then we'll see tomorrow morning how he feels and what we will do. That he has arrived here at the finish on the bike is already a good thing, but now we just need to be sure because the Ardennes, our big goals, are coming up. We will see tomorrow morning.
"It's hard to tell what happened," Lodewyck said. "The guys were all in a good position in front and suddenly the peloton swings from the right side to the left side. Mas told us a guy tried to get in between and pushed too hard and the front wheel went away and boom, there he goes.
"We were pulling all day with different teams who helped us, and with teams who didn't help us, and they were pretty fresh at the end," Lodewyck said. "They also knew that we were the big favourite again and they just want to beat us, and everything gets very stressful and dangerous at the end."