At first I thought there might have been a typo, but the original does say "Dentro de poco sonará la oración
en los Templarios", so this is not an error.
Later in the text, Alonso says: "¿Oyes? Las campanas doblan, la oración ha sonado
en San Juan del Duero..."
In this context, "la oración" is the worship service for the deceased, the bells toll in the church to make the faithful attend the mass.
For me, "sonará la oración en los Templarios" means that bells calling to mass will be heard from the monastery where the Templars are buried, signaling that they're coming to life again, or that the call for prayer will raise them from their tombs.
If we say "...la oración
de los Templarios", it's them who are praying, but then we know they're actually fighting.
Bécquer is not an easy author to read, so keep asking questions if you need to. We're glad to help.