Since the Bourbaki style is terrible to track down all the detals, I post this one to help others those who want to read a full proof of this problem; of course, I adapt modern notations.
Fix a base $\Delta$ for the root system $\Sigma$. Denote
$$\Sigma^* = \left \{\alpha^* \mid \alpha \ \text{is a root} \ \right \}$$
$$\mathrm{Aut}(\Sigma^*,\Delta) = \left \{ \ \text{elements in} \ \mathrm{Aut}(\Sigma^*) \ \text{stabilize} \ \Delta \right \}.$$
We are now at the position to prove that if $\phi \in N$ s.t. $\psi(\phi)$ induces an element in $\mathrm{Aut}(\Sigma^*,\Delta)$ then $\delta=\psi(\phi)$ is induced by an element in $Z = \left \{\phi \in \mathrm{Aut}_0(\mathfrak{g}) \mid \phi_{\mid \mathfrak{h}} = \mathrm{id}_{\mid \mathfrak{h}} \right \}$. The subgroup generated by $\delta$ has a finite number of orbits on $\Sigma^*$, let $U$ be such an orbit of cardinal $r$, denote
$$g_U = \bigoplus_{\alpha^* \in U} g_{\alpha}.$$
Let $\alpha_1^*\in U$ and I define $\alpha_i^* = \delta^{i-1}(\alpha_1^*) = (\alpha_1 \circ \delta^{1-i})^* \ \forall \ i = \overline{1,r}$. Thus $U = \left \{\alpha_1^*,...,\alpha_r^* \right \}$. Let $X_1$ b a non-zero element in $g_{\alpha_1}$. We are going to prove that there exists a non-zero scalar $c_U$ such that $\delta^r(X_1)=c_U X_1$. To do this, recall that $U$ is an orbit, therefore $\delta^r(\alpha_1^*) = \alpha_1^*$, equivalently, $(\alpha_1 \circ \delta^{-r})^* = \alpha_1^*$. We claim that $\delta^r(X_1) \in g_{\alpha_1}$. Indeed, for all $H \in \mathfrak{h}$,
$$\begin{align*}
[H,\delta^r(X_1)] & = \delta^r[\delta^{-r}(H),X_1] \\ & = \delta^r\left((\alpha_1\circ \delta^{-r})(H)X_1 \right) \\& = (\alpha_1\circ\delta^{-r})(H) \delta^r(X_1) \\ & = B(H,(\alpha_1 \circ \delta^{-r})^*) \delta^r(X_1) \\ & = B(H,\alpha_1^*)\delta^r(X_1) \\ & = \alpha_1(H)\delta^r(X_1). \end{align*}$$
But by the semisimplicity of $\mathfrak{g}$, $\mathrm{dim}(g_{\alpha})=1$, hence $\delta^r(X_1)$ and $X_1$ are proportional, prove our claim. By the definition of other $X_i$, we deduce that
$$\delta^r_{\mid g_U} = c_U.\mathrm{id}_{g_U}.$$
We shall twist $\delta$ by an element of $Z$ so that the resulting automorphism still comes from an element in $Z$. For each functional,
$$\Theta: \bigoplus_{\alpha \in \Sigma} \mathbb{Z}\alpha^* \to \mathbb{C}^*$$
We define an element $Z$, denoted by $f(\Theta)$, by the following rule
$$\begin{cases} f(\Theta)_{\mid g_{\alpha}} = \Theta(\alpha^*)\mathrm{id}_{\alpha} \\ f(\Theta)_{\mid \mathfrak{h}} = \mathrm{id}_{\mathfrak{h}} \end{cases}$$
It is clear that $f(\Theta) \in Z$. Moreover,
$$(\delta \circ f(\Theta))(X_1) = \delta(\Theta(\alpha_1^*)X_1) = \Theta(\alpha_1^*)\delta(X_1) = \Theta(\alpha_1^*)X_2.$$
Iterating this process by successively applying $\delta \circ f(\Theta)$, we deduce that
$$(\delta \circ f(\Theta))^r(X_1) = c_U\prod_{i=1}^r \Theta(\alpha_i^*)X_1 = c_U \Theta \left(\sum_{i=1}^r \alpha_i^* \right)X_1.$$
Again, this implies that
$$(\delta \circ f(\Theta))^r_{\mid g_U} = c_U \Theta \left(\sum_{i=1}^r \alpha_i^* \right) \mathrm{id}_{g_U}.$$
Let write our fixed base $\Delta$ as $\Delta = \left \{\beta_1^*,...,\beta_n^* \right \}$. Since this is a base, there exists $a_1^U,...,a_1^U \in \mathbb{Z}$, have same sign, not all zero such that $\alpha_1^*= \sum_{i=1}^n a_i^U \beta_i^*$, successively apply $\delta$ and recall that $\delta \in \mathrm{Aut}(\Sigma^*,\Delta)$ we deduce the existence of $m_1^U,...,m_n^U \in \mathbb{Z}$ of same sign, not all zero such that
$$\sum_{i=1}^r \alpha_i^* = \sum_{i=1}^n m_i^U \beta_i^*.$$
Thus, define $c'_U = c_U\Theta \left(\sum_{i=1}^r \alpha_i^* \right) = c_U \prod_{i=1}^n \Theta(\beta_i^*)^{m_i^U}$, we can choose $\Theta$ such that for all orbits $U$, $c_U' \neq 1$. This is possible, because it is equivalent to choose $\Theta(\beta_i^*) = t_i$ are elements in $\mathbb{C}^*$ such that all polynomial $c_U\prod_{i=1}^n t_i^{m_i^U} - c'_U$ vanish. So far, what we've done is to show that it is possible to choose $\Theta$ such that $\delta \circ f(\Theta)$ does not have $1$ as an eigenvalue on the subspace $\oplus_{\alpha \in \Sigma} g_{\alpha}$.
Now since $\mathrm{Aut}^0(\mathfrak{g})$ is a connected Lie group, every element can be written as product of some $e^{y}$ with $y \in \mathrm{Lie}(\mathrm{Aut}^0(\mathfrak{g})) \subset \mathrm{Der}(\mathfrak{g}) \overset{\text{semisimplicity}}{=} \mathrm{ad}(\mathfrak{g})$; thus, each element in $\mathrm{Aut}^0(\mathfrak{g})$ is a product of elements of form $e^{\mathrm{ad}(x)}$ with $x \in \mathfrak{g}$. We are at the position to prove that the generalized $0$-space of $\delta \circ f(\Theta) - \mathrm{id}$ has dimension at least the dimension of $\mathfrak{h}$, which equals $\mathrm{rank}(\mathfrak{g})$. To illustrate how to do this, we consider the case $\delta \circ f(\Theta) = e^{\mathrm{ad}(x)}$ only. Since we are working over $\mathrm{C}$, $\mathrm{ad}(x)$ is similar to a Jordan matrix $J$, read $\mathrm{ad}(x) = AJA^{-1}$ for some $A \in \mathrm{GL}(\mathfrak{g})$. Thus, $\mathrm{dim} \mathfrak{g}^0(\mathrm{ad}(x))$ is precisely the number of $0$ on the diagonal. Moreover, $e^{\mathrm{ad}(x)} - \mathrm{id} = A(e^J - 1)A^{-1}$ and $e^{\lambda}=1 \Leftrightarrow \lambda=0$, we conclude that the number of $0$ on the diagonal of $e^J - \mathrm{id}$ equals of $\mathrm{ad}(x)$. Finally
$$\mathrm{dim} \bigcup_{k \geq 1} (\delta \circ f(\Theta) - \mathrm{id})^k = \mathrm{dim} \mathfrak{g}^0(\mathrm{ad}(x)) \geq \mathrm{rank}(\mathfrak{g}) = \mathrm{dim}\mathfrak{h}.$$
By the assumption of no eigenvalue $1$ on the complement $\oplus_{\alpha \in \Sigma}g_{\alpha}$, we see that $\delta \circ f(\Theta) - \mathrm{id}$ is nilpotent on $\mathfrak{h}$. On the other hand, $\delta \circ f(\Theta)$ permutes a base so it has finite order (it is an element of a finite symmetric group). Consequently, its characteristic polynomial (and hence minial polynomial) divides $x^k-1$ for some $k$, the latter polynomial has all roots as simple roots so the Jordan blocks of $\delta \circ f(\Theta)$ are all of size $(1 \times 1)$; i.e. $\delta \circ f(\Theta)$ is diagonalizable. Combine this with the previous assertion of $\delta \circ f(\Theta)$ being nilpotent, we deduce that $\delta \circ f(\Theta)_{\mid \mathfrak{h}} = \mathrm{id}_{\mathfrak{h}}$, as desired.