* San José, Costa Rica
* San Salvador, El Salvador
* San Juan, Puerto Rico
* Santiago, Chile
* Santo Domingo, Dominican Republic
While not technically a capital, San Marino is a microstate with a Spanish-speaking population and a name derived from Saint Marinus.
It's worth noting that many other Spanish-speaking cities and towns also have names derived from saints. This is a reflection of the strong influence of Catholicism in the region.