This is easiest done not using index notation. Define the column vector
$$
\vec{\phi} =
\begin{pmatrix}
\phi_1 \\ \phi_2 \\ \phi_3
\end{pmatrix}
$$
The derivative acts on the column vector as $\mathbf{1}_3\partial_\mu$ where $\mathbf{1}_3$ is the identity matrix on the same vector space in which $\vec{\phi}$ lives. That is,
$$
\partial_\mu \vec{\phi} =
\begin{pmatrix}
\partial_\mu \phi_1 \\ \partial_\mu \phi_2 \\ \partial_\mu \phi_3
\end{pmatrix}
$$
Then we can write the lagrangian as
$$
\mathcal{L}=\frac{1}{2}(\partial_\mu \vec{\phi})^T (\partial_\mu \vec{\phi}) - \frac{1}{2}\vec{\phi}^T \vec{\phi}
$$
Now it can be seen basically by inspection that for $R\in SO(3)$ we have that
$$
\vec{\phi} \stackrel{SO(3)}{\longmapsto} R\vec{\phi} \tag{(a)}\\
\vec{\phi}^T \stackrel{SO(3)}{\longmapsto} \vec{\phi}^T R^T
$$
Under this transfermation, both terms in the lagrangian both terms pick up an $R^TR = \mathbf{1}_3$ sandwiched in the middle. Hence the lagrangian is invariant.
Relating to the transformation law using index notation:
$$ \phi_a \to \phi_a + \theta \epsilon_{abc}n_b\phi_c $$
A general $SO(3)$ transformation can be written as
$$
R = e^{-iL_an_a \theta}
$$
so that an infinitesimal transformation can be written as
$$
R = 1 -iL_an_a \theta + \mathcal{O}(\theta^2)
$$
Now, in the fundamental representation the generators are given by
$$
(L^a)_{bc} = -\epsilon_{abc}
$$
We therefore see that an infinitesimal SO(3) transformation on $\phi_a$ is given as
$$
\phi_a \to R_{ab}\phi_b = \phi_a + i\theta\epsilon_{abc}n_c \phi_b + \mathcal{O}(\theta^2) \tag{b}
$$
So we see that proving the lagrangian is invariant under (b) is a special case of proving it is invariant under (a).