The Bible makes several references to practicing Astrology to detect holy events, including the Magi finding Jesus, and David predicting the future. It seems like god is directly endorsing astrology, yet today it is considered satanic or an evil act by many Christian practitioners. What caused this shift?
Edit: I'm not aware of the Catholic church taking an official stance on astrology, this reflects more the general sentiment.
The phrasing of the question makes an argument which is not true: that astrology 'equaled' witchcraft at some point in time. This was never the case, at least in a European-North American context.
The first point, about witchcraft: astrology was never considered witchcraft in and of itself at any point as a matter of broad policy, neither by secular nor religious law. Here we can talk about late medieval through early modern period (note that accusations of witchcraft were rare in the medieval period before 1300), and we will speak very broadly.
Accusations of witchcraft, over the course of hundreds of years and in different localities, was generally a question of effect or result, and then complainants would look for cause and evidence. So, someone would be accused of causing someone's death, causing an animal or crops to die, or causing various manners of injury to person or property. From there might proceed an accusation of being a witch (or necromancer, or sorcerer) and simultaneously finding sources to support the accusation. Those sources could be any of a wide-ranging collection of indicators: herbal remedies, songs and incantations, strange looks, and yes, astrology could be rolled up in it.
Astrology continued to have a life long into the early modern period, even within monestaries and priesthood, sometimes forbidden, sometimes permitted. Astrology had a life even within Christian royal and noble circles across Europe.
To summarize: astrology was never the foundation of witchcraft accusations, it could be (rarely) dredged up as convenient support for the accusation. What's most important to understand about witchcraft accusations in this context is that anything could be used as evidence for an accusation so long as the community supported it being transformed into an act or habit of a witch. Being astrology, as a thing unto itself, was not especially relevant.
As a side note, astrology as a going concern was really demolished by scientific understanding of stars, planets, et al in the latter part of the early modern period, in particular the 17th century.
For a very readable introduction to astrology and magic in the middle ages: