Note: 祈る may appear in various conjugations (祈っている, 祈ります, etc.)
The structure ようにいのる (ように祈る) is used to express praying, hoping, or wishing that something will happen (or won't happen). It conveys a heartfelt desire directed toward an outcome that is often beyond one's direct control.
The verb before ように is typically in the plain non-past form (dictionary form for positive wishes, ない-form for negative wishes).
Use Verb[dictionary form] + ように祈る to pray or hope that something will come true.
Use Verb[ない-form] + ように祈る to pray or hope that something won't occur.
This expression is used in contexts like making wishes at shrines or temples, sending well-wishes to someone, or expressing sincere hope for a future outcome. It is stronger and more earnest than simply saying といいな ("I hope…") and carries a sense of genuine prayer or deep wish.
The verb いのる祈る itself can be conjugated freely – いのります祈ります (polite), いのっている祈っている (ongoing/state), いのった祈った (past), etc.
A common related pattern is ように願う (to wish that), which is very similar in meaning but slightly less associated with prayer specifically.