1999 World Cup victory-

Australia then had a slow start to the 1999 World Cup in England. After a scratchy win against Scotland, Australia suffered defeats to New Zealand and Pakistan, so they had to win their two remaining group matches (against Bangladesh and the West Indies), then all three "Super Six" matches to progress to the semi-finals: this meant seven consecutive matches without defeat to win the World Cup. After defeating Bangladesh, Waugh and Michael Bevan were criticised for deliberately batting slowly in order to minimise damage to the net run rate of the West Indies. This would enhance Australia's chances: if the West Indies' run rate remained high, they would qualify ahead of New Zealand. Since the Australians had lost to New Zealand, it would be the Kiwis that carried two points through to the next phase if the West Indies was eliminated. If the West Indies proceeded, then Australia would carry over two points from the win.

When questioned about the ethics of this manipulation at a press conference, Waugh retorted, "We're not here to win friends mate". Having beaten India and Zimbabwe in their first two Super Six matches, Waugh saved his best for two must-win games against South Africa: he scored an unbeaten 120 against South Africa in the "Super Six" phase and 56 in the semi-final. The latter match was tied and Australia progressed to the final, where they crushed Pakistan by eight wickets to win the trophy.

The World Cup victory did not immediately turn around Waugh's fortunes in the Test arena. The following tour to Sri Lanka continued the difficulties, when Australia lost the First Test at Kandy, a result exacerbated by a horrific fielding collision between Waugh and Jason Gillespie. Waugh's nose made contact with Gillespie's shin as both attempted a catch. Gillespie suffered a broken leg that sidelined him for 15 months, and Waugh had his nose broken. Although Waugh returned for the following match, the last two Tests were drawn due to interruptions from monsoonal weather. In losing 0–1, the Australians struggled to combat the bowling of Muttiah Muralitharan. Waugh had a lean series with 52 runs at 17.33. Waugh's team then travelled an inaugural Test against Zimbabwe at Harare. Australia won by ten wickets and Waugh's 151 not out was the first century in Tests between the nations. After the team's return home, John Buchanan replaced Geoff Marsh as team coach.