With the answer and the comments I finally could answer the question by myself and solve my confusion. Thanks again for putting me on the right track. Both leads to a valid solution.
Edit: And as user amsmath commented, it always holds that $min_{||x||=1}||Ax|| = min_{||x||=1}\sqrt{\langle A^TAx, x \rangle}$ which is always (!) the square root of the smallest eigenvalue of $A^TA$ (and at the same time the smallest singular value of $A$)
An overdetermined homogeneous linear equation system can be represented as $Ax=0$, where $A\in R^{m\times n}$ with $m>n$ subject to $||x||=1$. Desired is a non trivial solution ($x\neq 0$), which minimizes $||Ax||$. Solutions form a hyperspace. If $x_0$ is a solution, then $\kappa x_0$ for $\kappa \in R$ is also a solution.
Case 1 - Solution is the right-singular vector corresponding to the smallest singular value of $A$
Edit: I was mixing up eigenvalues and singular value. Beeing precise helps to improve understanding. In that post the difference of eigenvalues and singular values is discussed.
We are looking for an $x$ that minimizes $||Ax||$ subject to $||x||$. The SVD decomposition of $A$ leads to $$A = UDV^T,$$ where $U\in R^{m\times m}$, $D\in R^{m\times n}$, and $V \in R^{n\times n}$.
Since $U$ is an orthogonal matrix $$||Ax||=||UDV^Tx||$$ leads to $$||Ax||=||DV^Tx||.$$
$V$ is also an orthogonal matrix. So if $||x||=1$ holds, then $||V^Tx||=1$ holds, too. We substitute $V^Tx$ with $y$ and minimizing $||Dy||c$ subject to $||y||=1$. The matrix $D$ is a diagonal matrix $$D=\begin{pmatrix} d_1 & 0 & \dots & 0\\
0 & d_2 & \dots & 0\\
\vdots & & \ddots & \vdots\\
0 & 0 & \dots & d_n\\
0 & 0 & \dots & 0\\
\vdots & \vdots & & \vdots\\
0 & 0 & \dots & 0\\
\end{pmatrix}\in R^{m\times n},$$ with $d_1 > d_2 > \dots > d_n$ we can minimize $||Dx||$ by chosing $$y = \begin{pmatrix}0\\0\\ \vdots \\ 1\end{pmatrix} \in R^{n\times 1},$$ which satisfy $||y||=1$.
The substitution of $V^T$ with $y$ leads to $$x=Vy=\begin{pmatrix}V_{1n}\\V_{2n}\\\vdots\\V_{nn}\end{pmatrix}$$ $\square$
Case 2 - Solution is the eigenvector corresponding to the smallest eigenvalue of $A^TA$.
Applying Lagrange function \begin{align}L(x,\lambda) & := ||Ax|| + \lambda (1-||x||) \\& = x^TA^TAx + \lambda (1-x^Tx) \end{align}
Critical points of the Lagrange function are found by equaling derivatives to zeros
\begin{align}
\frac{\partial L(x,\lambda)}{\partial x} & = 2A^TAx - 2\lambda x = 0\\
\frac{\partial L(x,\lambda)}{\partial \lambda} & = 1- x^Tx = 0
\end{align}
First partial derivative can be rewritten as the characteristic polynom $$(A^TA - \lambda I)x = 0$$ of $A^TA$. So every eigenvector $x$ with corresponding eigenvalue $\lambda$ is a critical point and hence a solution for the equation above. We choose the smallest eigenvalue to minimize $||Ax||$.
Combining equations lead to
\begin{align}||Ax|| &= x^TA^TAx \\
&= x^T\lambda x\\
&= \lambda x^Tx\\
&=\lambda||x||\\&
= \lambda
\end{align}
Therefore the solution is the eigenvector of $A^TA$ with the smallest corresponding eigenvalue.
$\square$