Since you already created all the necessary vertices for the holes you can do the following, if the face you want to cut is flat and all the vertices for the holes lie in the same plane as the main face:
Holes in faces need supporting edges. Press K and use the Knife tool to make two cuts from one border of the face to the opposite side so that they cross through the "soon-to-become-holes".
The Knife doesn't need to cut the hole shapes - you only need the edges across. Now select all vertices with A. Enable the Auto Merge function at the top right of the 3D Viewport and make sure that under Options > Split Edges & Faces is enabled.
Next you press G followed by 0 (zero) so that the Move tool is theoretically moving the vertices, but they stay in place (do not abort the movement with right-click or Esc). Confirm the movement with Return or left-click.
After this operation, the vertices are cut into the face. You can now select the inner faces and delete them with X > Delete > Faces to get the holes.
Just a quick note: if the "hole vertices" are just edges, the faces can simply be selected and deleted because the underlying face got split up into these faces. If the "hole vertices" are shapes filled with faces themselves, you'll get double faces where the holes: the original faces of the hole shapes and the cut faces of the underlying plane, so you have to delete them both to get a hole.
And one more thing: If you let the Auto Merge function enabled after this, it might happen you accidentally merge and split vertices and faces just by moving, rotating or scaling something which can mess up your mesh. So I would recommend to disable this function after creating the holes.