Having returned home, Kruger was surprised to receive a message urgently requesting his presence in the capital, the volksraad having recommended him as a suitable candidate.

Van Rensburg promptly had legislation passed to give equal political rights to members of all Reformed denominations.

After Schoeman returned with a larger force Kruger and Pretorius held negotiations and agreed to hold a special court on the disturbances in January 1863 and soon thereafter fresh elections for president and commandant-general.

[5] The civil war ended with Kruger's victory over Jan Viljoen's commando, raised in support of Pretorius and Schoeman, at the Crocodile River on 5 January 1864.

[6] The civil war led to an economic collapse in the Transvaal, weakening the government's ability to back up its professed authority and sovereignty over the local chiefdoms,[7] though Lydenburg and Utrecht now accepted the central administration.

The Basotho were defeated and Moshoeshoe ceded some of his territory, but President Johannes Brand of the Free State decided not to give any of the conquered land to the Transvaal burghers.

The Transvaal government formally exonerated Kruger over the matter by ruling that he had been forced to evacuate Schoemansdal by factors beyond his control, but some still argued that he had given the town up too readily.

In the 1872 election Kruger's preferred candidate, William Robinson, was decisively defeated by Thomas François Burgers, a church minister from the Cape who was noted for his eloquent preaching but controversial because of his liberal interpretation of the scriptures; for example, he did not believe in the Devil.

[11][n 1] Kruger publicly accepted Burgers's election and announced at his inauguration that "as a good republican", he submitted to the vote of the majority but had grave personal reservations regarding the new president.

[11] He particularly disliked Burgers's new education law, which restricted children's religious instruction to outside school hours, which was in Kruger's view an affront to God.