Basically, an unmatched glut of violence brought an end to the (explicitly) internecine violence. Something to consider is that Christian-on-Christian violence did not begin with the Reformation—the Albigensian Crusade of the early 13th century and the Hussite Wars of the 15th are examples of serious military exercises before the Reformation split the Catholic Church permanently. It's also worth noting that, even after the formal end of explicit violence over religious matters (with the end of the Thirty Years' War), confessional identity was still part of the underlying political milieu that drove diplomacy. A final note: in pre-modern times, distinguishing between religious and political considerations is a fairly impossible task. As a result, I'll just be focusing primarily on conflict explicitly founded over different branches of Christianity.

Back on track: as you note, in the wake of the Reformation, violence between Christians over matters of religion hit an all-time high. This peaked with the Thirty Years' War, which all but destroyed Germany (by some estimates, a third of its population was killed, died via disease or starvation, or forced to flee). Before this, there were a number of smaller wars that can be pinned strongly on religious conflict: on the Continent, mainly the Schmalkaldic War, the Cologne War, and the French Wars of Religion.

So, for roughly a century (1546-1648), the Continent was either prepared for war over religion or at war over religion. The first bout of armed conflict was ended with the Peace of Augsburg in 1555, which established cuius regio, eius religio (who rules, his religion), that legally allowed princes of the Holy Roman Empire to determine the state religion—only Lutheranism and Catholicism were included in this decision, as Calvinists were still a relatively small minority. Moreover, the Peace of Augsburg gave no protection for worshipers of the "wrong" faith within a prince's territory.

The Thirty Years' War began largely as a result of that lack of protection: Protestantism, which had taken root among the nobility in the Catholic Habsburg lands (the Habsburg dynasty were Holy Roman Emperors), was being snuffed out from these places by the Catholic Counter-Reformation. Once the war began, Emperor Ferdinand II made it his goal after swift major successes to move to cleanse the entire Empire of Protestantism. This conflict first broke the power of the Protestant princes, who were then supported by the Protestant Danish King, and then the Protestant Swedish King (the famed Gustavus Adolphus). When these two ultimately failed to defeat the Catholic forces of the Habsburgs and their allies, the Catholic French (under Cardinals Richelieu and Mazarin) would enter against the Habsburgs and finally break their power on the Continent.

The horrors of the Thirty Years' War, and the religious conflicts in this period generally, are hard to overstate. Nearly the entire city of Magdeburg was put to the sword in 1630, the St. Bartholomew's Day Massacre in France led to the death of many thousands of Huguenots, and the simple prosecution of the wars themselves led to vast destruction on a scale not seen until the Second World War. All told, the Wars of Religion during this period claimed well over 10 million lives when the whole population of Europe was under 100 million.

So, when time came to discuss peace, all parties had a strong interest in making a lasting settlement to the "religious question". Armed conflict had proven wholly incapable of answering the question, and delegates of the involved powers met in Münster and Osnabruck, in the region of Westphalia, to discuss such a peace. The Peace of Westphalia, as the treaties the powers signed are known, re-established the principle of cuius regio, eius religio. However, it added two equally important ideas: states were declared sovereign and religious minorities within a state (including Calvinism) were to be allowed to practice their religion within certain bounds.

The Peace of Westphalia was successful in its goal of ending explicit religious conflict: ultimately, maintaining the "balance of power" between states became a larger motivation for conflict than religious ties, and religious toleration, by which, contrary to the modern definition, I mean that the different sects merely put up with one another, became the norm across Europe. The doctrine of state sovereignty implied that the threat to one prince's right to self-determination was a serious matter regardless of his religious beliefs. While alliances still tended to fall along confessional lines, military force was no longer a legitimate tool to achieve internecine aims.

What makes you think it's ended? There is an argument that the Northern Ireland "Troubles" are at least in part religious - in name if not theologically