Pablo Fornals scored the only goal of the second leg as the Hammers made it into a first European final for 47 years.
The Spaniard’s goal wrapped up a 3-1 aggregate win over the Dutch side and sparked wild scenes of celebrations from the West Ham players on the pitch at AFAS Stadion.
Still, the historic result for the east London club was marred by horrific scenes after the game.
A group of Alkmaar supporters appeared to attack a section of the traveling support in an area in which the families and friends of West Ham players and staff were sat.
Several members of Moyes’s squad weighed in to protect their loves ones, who had broken through a barrier to race around the pitch.
“I can’t explain what happened or why it happened,” said Moyes.
“I can only tell you that players were involved because it was the family section, where most of their family and friends were sat in. I think that is why, seeing friends and family in that area.
“That was probably the reason for the reaction. What I don’t want in any way is that to blight tonight because it wasn’t the West Ham fans who were looking for trouble. They were happy to celebrate at the end of the game. Hopefully, they will look into and find the reasons why.
“My family were there and I had friends in that section.
“I think you’re hoping they would try and get themselves away from it, I had a couple of friends in that area.
“I didn’t recognise it because I was too happy to go on to the pitch and see the other people and the referee before I left. Security wanted to take me inside but I had to make sure the players were not going to get involved in it.”