Perhaps there is a stronger version states that one can shift $F$ by a rational number $q$ such that the intersection is of positive measure.
Apply Lebesgue's density theorem on both $E$ and $F$. We find that there exists $x$ and $\epsilon$ such that $m(E\cap B(x,\epsilon/2))>3\epsilon/4$. For the same reason there exists $y$ such that $m(F\cap B(y,\epsilon/2))>3\epsilon/4$; take a smaller $\epsilon$ if necessary. Now we choose a rational $q$ from $B(x-y,\epsilon/4)$.
Consider intersections
$$E':=E\cap B(x,\epsilon/2)\subset B(x,\epsilon/2),\qquad F':=(F+q)\cap B(y+q,\epsilon/2)\subset B(y+q,\epsilon/2).$$
By how we take $x,\epsilon$ it is clearly that $E'$, comparing to $B(x,\epsilon/2)$, loses $1/4$ of its mass. Also, $F'$, comparing to $B(y+q,\epsilon/2)$, loses $1/4$ of its mass. Forming the intersection $E'\cap F'$ will loses another 1/4 by how we take $q$. Combining these three inequalities and Boole's inequality we see that $E'\cap F'$ is of positive measure and so is $E\cap F$.