I don't think this has anything to do with the integral. If $S=S^T$ then
\begin{align}
S : \nabla \phi = \sum_{i,j} S_{ij} \partial_j \phi_i
&= \frac12\left(\sum_{i,j} S_{ij} \partial_j \phi_i + \sum_{i,j} S_{ij} \partial_j \phi_i\right) \\
&= \frac12 \left(\sum_{i,j} S_{ij} \partial_j \phi_i + \sum_{i,j} S_{\color{red}{ji}} \partial_j \phi_i\right)\\
&= \frac12 \left(\sum_{i,j} S_{ij} \partial_j \phi_i + \sum_{j',i'} S_{i',j'} \partial_{i'} \phi_{j'}\right) \\
&= \sum_{i,j}S_{ij} \frac12 \left( \partial_j \phi_i + \partial_i \phi_j \right)\\
&= S : D(\phi).
\end{align}
Or, if you prefer to see less indices, since $A^T:B = A:B^T$
\begin{align} S: \nabla \phi &= \frac12(S + S^T ): \nabla \phi \\
&= \frac12\left(S:\nabla \phi + S^T: \nabla \phi\right) \\
&= \frac12\left(S:\nabla \phi + S: \nabla \phi^T\right) \\
&= S : \frac12(\nabla \phi + \nabla\phi^T)\\ & = S:D(\phi).
\end{align}