We can prove this by imagining reassembling the polyhedron from its faces. In particular, consider that an $n$-gon face consists of $n$ vertices, $n$ edges and one face and hence has an "Euler characteristic" of $n-n+1=1$. So, when we set in place our first face, we have Euler characteristic one.
Next, we line up another face of the polygon such that it shares an edge with the original one, and we glue it up real nice and such - now, naively, since we just added another polygon, which has Eulcer characteristic one, we would expect the characteristic of this figure would be $1+1=2$ - however, we need to correct for the fact that the two faces share $2$ vertices and $1$ edge, implying that our characteristic is $(2-1+0)=1$ higher than it ought to be - so it still has characteristic one.
Next, we can proceed to choose one of the vertices shared between these first two shapes, and one by one add all the faces around this vertex. In general, these new faces will share $2$ vertices and $1$ edge and with the previously existing shape (and will add a face), leaving the Euler characteristic unaltered. However, when we put in the last face required to enclose this vertex, it will adjoin to two edges (completing a little cycle around the vertex), and thus share $3$ vertices and $2$ edges with the previous shape - which still leaves the characteristic unchanged, mind you.
More generally, if a new face joins with $n$ pre-existing edges, we want it to be true that it will share $n+1$ vertices with the pre-existing shape. To do this, we need that those $n$ pre-existing edges form a path between $n+1$ of vertices of the added shape. If this didn't happen, it would mean that there were two, disconnected, places where the new face intersected the previous shape - thus creating a "hole" in the figure (read: the shape wouldn't be simply connected). Rather than try to deal with this, we just notice that we can always avoid creating a hole, and thus decide that we will never create a hole while making the figure, ensuring that our invariant is actually invariant.
Then, using this method, we can build up the shape minus a single face, and it will have characteristic $1$. However, when we join the new face on, it will line up with all its vertices and edges - thus will leave $V$ and $E$ unchanged - but it constitutes a new face, increasing the characteristic to $2$.
This may be difficult to visualize on paper - but I have a solution to that: You can carry out this construction physically and watch it work.