Simply put, they never did. Protestants of the Calvinist (often times called Reformed) tradition remain a significant force in Germany today, under the umbrella of the Evangelical Church of Germany, which includes for the most part all major protestant groups in the country, Lutherans and Calvinists included. For certain, Calvinism was never replaced by anything; it coexisted with Lutheranism and Catholicism as established by the Peace of Westphalia in 1648. As for the history of the matter, I can really only go into a decent amount of detail in regards to religion in Prussia.

Traditionally, the peasants and major landowners in Brandenburg were Lutheran. However, in 1616 the elector of Brandenburg, John Sigismund, disillusioned with Lutheranism converted to Calvinism. He and his advisers envisioned a sort of second Reformation, during which Brandenburg's Lutheran population would hop onto the Calvinist bandwagon. Unfortunately for Sigismund, this didn't happen. There was a major backlash – not even his wife would convert! – and eventually he reluctantly agreed to allow Lutherans to keep their faith. Sigismund's grandson, Frederick William “The Great Elector” (ruled 1640-88) guaranteed Lutherans repeatedly that the monarchy would not impose its beliefs on the population, and Prussia emerged as a bi-confessional state. Also worthy of mention is that near the end of the Great Elector's reign, Louis XIV of France revoked the Edict of Nantes, which had allowed French Calvinists (Huguenots) to remain in France. The Elector opened the doors and allowed a flood of Calvinists to enter Brandenburg-Prussia, so the country wasn't just a whole bunch of Lutherans with a Calvinist monarchy, but a realm with a significant Calvinist minority with a Calvinist monarch. Many of those Calvinists and their descendents remain in Germany today. Merkel's current Minister of the Interior, Thomas de Maizière, is one such descendent.

The Great Elector realized the tolerating different confessions in his state had pragmatic benefits. His successors followed suit, and Brandenburg-Prussia became known as a place where Protestants of all kinds could flee to. In the 1730s, for example, a number of protestants fled Catholic Salzurg in the south for Prussia. To a certain extent, even Jews were tolerated in Berlin.

Frederick the Great's nephew, Frederick William III (ruled 1786-97) attempted to beat back the advances of the Enlightenment during his reign. His tenure saw an increasing grip on both Lutheran and Calvinist camps by the state in order to retain control of the population. This policy was continued by his son, Frederick William III (ruled 1797-1840). The first twenty or so years of his reign saw an a rise of protestant fundamentalism, during which many “Awakened” Christians refused to attend either of the establish Protestant churches. Recognizing this as a potential threat to state stability, Frederick William III announced in 1817 that he would be the head of a new church, which would be an “evangelical Christian” church. Basically, he wanted to unite the Lutheran and Calvinist faiths so religious fundamentalism would be less of a problem. Through a hodgepodge of Lutheran and Calvinist texts, the Church of the Prussian Union was born with the Hohenzollern monarch at its head. Not everyone was a fan of this arrangement, including a group of Lutherans that were dubbed “Old Lutherans.” They resisted the new Union, and attempts to force them to into the church resulted in mass emigration of Old Lutherans. Many of them ended up in America, where they formed the Lutheran Church-Missouri Synod. Realizing their mistake, albeit too late, Prussian officials eventually allowed dissident church goers to return and establish their own church. Today in Germany, we can see Old Lutheran theology in the Independent Evangelical-Lutheran Church.

So now in the beginning of the 19th century we see that Prussia finally has a unified church, which most people are more or less happy with (the dissenters having left). As Prussia acquired more territory through the century, the Church too expanded, though without the heavy handedness that scared away the Old Lutherans. When denominations were unwilling to the join the Union, they were allowed to do so. The Church of the Prussian Union remained the official church of Germany until the fall of the monarchy following World War I.

After the war, things get a little complicated and I'm not sure that I'm entirely qualified to speak on the matter. The church dealt with several schisms as a result of disagreements over the collaboration with Nazi officials, and church-goers faced significant prosecution in territories that were captured by the Soviets near the end of the war. For the most part, the Second World War broke the Church of the Prussian Union, and it fell to pieces. The successor to the Prussian Union is called the Evangelical Church in Germany (EKD), and it comprises basically all of the protestant churches in the country. This is not to say that there is a unified doctrine; Lutherans, Calvinists, and the remaining Prussian Unionists all run their own churches independently, but they recognize each other and share a certain degree of similarities. The different denominations do not compete for members with one another, as each church as a certain jurisdiction. For example, one town might be exclusively Lutheran, while another might be Prussian Unionist. Having said all this, I'm quite sure a native German could describe the EKD better than me, so I apologize. Today, most German protestants are part of the EKD.

Clark, Christopher M.. Iron kingdom: The Rise and Downfall of Prussia, 1600-1947. Cambridge, Mass.: Belknap Press of Harvard University Press, 2006.