I have a matrix $\Sigma$ given by \begin{equation*} \Sigma = \begin{bmatrix} \phi_{11} &\phi_{12}\\ \phi_{12} & \phi_{22} \end{bmatrix} \end{equation*}
I'd like to calculate the partial derivative by element, for example, $\frac{\partial y^T\Sigma^{-1} y}{\partial \phi_{11}}$,where $y$ is a vector.
First, computing the derivative of $\Sigma$ is straightforward $$ \frac{\partial\Sigma}{\partial \phi_{11}} = \begin{pmatrix} 1 & 0 \\ 0 & 0 \end{pmatrix}=E_{11} $$ To compute the derivative of $\Sigma^{-1}$ note that $\Sigma^{-1}\Sigma=I$, so by the product rule we have $$ 0 = \frac{\partial I}{\partial \phi_{ij}} = \frac{\partial \Sigma^{-1}\Sigma}{\partial \phi_{ij}}= \frac{\partial \Sigma^{-1}}{\partial \phi_{ij}}\Sigma + \Sigma^{-1}\frac{\partial \Sigma}{\partial \phi_{ij}} $$ Solving for $ \frac{\partial \Sigma^{-1}}{\partial \phi_{ij}}$ in this equation we get the answer that $$ \frac{\partial \Sigma^{-1}}{\partial \phi_{ij}} = -\Sigma^{-1}\frac{\partial \Sigma}{\partial \phi_{ij}}\Sigma^{-1}=-\Sigma^{-1}E_{ij}\Sigma^{-1} $$ If $y$ is independent of $\phi_{ij}$ that means the derivative of your expression would be $$ -y^{\top}\Sigma^{-1}E_{ij}\Sigma^{-1}y $$ Otherwise you would have to use the product rule.