I've looked at that too, even slowed it down frame-by-frame on the DVD (a Region 2 French disc), and still I can't quite see for certain what they did. Presumably they had a marksman shoot a fake arrow with a suction-cup tip that would stick to the actor's neck, which seems obvious and logical, but even in slow motion it's hard to see much clearly. The whole thing only took a second and it's still a bit blurred even when slowed down. But the effect is very realistic and cool-looking.
Pascal was played in his film debut by actor Booth Colman, who died last December at age 91. If you watch the scene closely, just before he's hit you can sort of tell he knows what's coming (as, obviously, he does), because he has a slightly frozen smile on his face and is somewhat stiff in his movements, clearly setting himself up for the arrow strike.
Definitely not an animated sequence -- Booth Colman's really being hit by a fake arrow. But it's damn convincing! You can still see it "in" him when he falls.
Maybe the other poster's Throne of Blood explanation is similar. But that was a much more involved take and most of the arrows stuck into Mifune's body area, where faking a hit is relatively easy. (They did a couple such shots in The Adventures of Robin Hood in 1938, for example.) Striking someone on his bare neck (which is also a much smaller target) is something else again.