Let $L= -\Delta+ V$ be a Schr\"odinger operator on $\mathbb R^d$, $d\geq 3$, where $V$ is a nonnegative potential, $V\ne 0$, and belongs to the reverse H\"older class $RH_{d/2}$. In this paper, we study the commutators $[b,T]$ for $T$ in a class $\mathcal K_L$ of sublinear operators containing the fundamental operators in harmonic analysis related to $L$. More precisely, when $T\in \mathcal K_L$, we prove that there exists a bounded subbilinear operator $\mathfrak R= \mathfrak R_T: H^1_L(\mathbb R^d)\times BMO(\mathbb R^d)\to L^1(\mathbb R^d)$ such that \begin{equation}\label{abstract 1} |T(\mathfrak S(f,b))|- \mathfrak R(f,b)\leq |[b,T](f)|\leq \mathfrak R(f,b) + |T(\mathfrak S(f,b))|, \end{equation} where $\mathfrak S$ is a bounded bilinear operator from $H^1_L(\mathbb R^d)\times BMO(\mathbb R^d)$ into $L^1(\mathbb R^d)$ which does not depend on $T$. The subbilinear decomposition (\ref{abstract 1}) allows us to explain why commutators with the fundamental operators are of weak type $(H^1_L,L^1)$, and when a commutator $[b,T]$ is of strong type $(H^1_L,L^1)$. Also, we discuss the $H^1_L$-estimates for commutators of the Riesz transforms associated with the Schr\"odinger operator $L$.