The Second Anglo-Boer War had no sooner commenced with the ultimatum of the Transvaal Republic on 9 October 1899, than Mr Schreiner found himself called upon to deal with the conduct of Cape rebels. The rebels joined the invading forces of President Steyn, whose false assurances Mr Schreiner had offered to an indignant House of Assembly only a few weeks before. The war on the part of the Republics was evidently not to be merely one of self-defence. It was one of aggression and aggrandisement. Mr Schreiner ultimately addressed, as prime minister, a sharp remonstrance to President Steyn for allowing his burghers to invade the colony. He also co-operated with Sir Alfred Milner, and used his influence to restrain the Bond.
The acknowledgment of defeat by the Boers in the field, and the surrender of some 10,000 rebels, did not weaken the endeavours of the Dutch to obtain political supremacy in the colony. Moreover, in the autumn of 1902 Sir Gordon Sprigg, the prime minister, nominally the leader of the Progressives, sought to maintain his position by securing the support of the Bond party in parliament. In the early part of 1903 Mr Chamberlain included Cape Town in his visit to South Africa, and had conferences with the political leaders of all parties. Reconciliation between the Bond and British elements in the colony was, however, still impossible, and the two parties concentrated their efforts on a struggle for victory at the coming election. Mr Hofmeyr, who had chosen to spend the greater part of the war period in Europe, returned to the Cape to reorganize the Bond. On the other side Dr Jameson came forward as the leader of the Progressives. Parliament was dissolved in September 1903. It had passed, since the war, two measures of importance - one (1902) restricting alien immigration, the other (1903) ratifying the first customs convention between all the South African colonies. This convention was notable for its grant of preferential treatment (in general, a rebate of 25% on the customs already levied) to imports from the United Kingdom.
The election turned on the issue of British or Bond supremacy. It was fought on a register purged of the rebel voters, many of whom, besides being disfranchised, were in prison. The issue was doubtful, and each side sought to secure the support of the native voters, who in several constituencies held the balance of power. The Bondsmen were more lavish than their opponents in their promises to the natives and even invited an African journalist (who declined) to stand for a seat in the Assembly. In view of the agitation then proceeding for the introduction of Chinese coolies to work the mines on the Rand, the Progressives declared their intention, if returned, to exclude them from the colony, and this declaration gained them some native votes. The polling (in January and February 1904) resulted in a Progressive majority of five in a house of 95 members. The rejected candidates included prominent Bond supporters like Mr Merriman and Mr Sauer, and also Sir Gordon Sprigg and Mr A. Douglass, another member of the cabinet. Mr W. P. Schreiner, the ex-premier, who stood as an Independent, was also rejected.