In this work, we settle a problem that dates back to the early 2000s. We provide a complete characterization of special matchings of arbitrary Bruhat intervals in Coxeter groups of type $A$ and apply this result to prove a conjecture of Brenti from 2003 concerning the computation of Kazhdan-Lusztig $R$-polynomials via special matchings. This yields new evidence in support of the Combinatorial Invariance Conjecture.