Think your are mixing up 1996 and 1999, Pakistan was expected to win 1996, SA was the clear favorite in 1999.
Pak lost 3 other games in 1999 apart from the final, against Bangladesh, India and South Africa. They went 6-4 in that WC, not exactly dominating. Great bowlers and all rounders but the batting was pretty poor in that WC. Misfiring middle order and a disaster tournament for Inzi, only Anwar was the saving grace. The other opener was Wajatullah Wasti and number 3 was Razzaq in those swinging conditions. Always prone to collapse which Australia ruthlessly exploited in the final.
No shame in losing to that legendary Aussie side, that was the tournament where their era of domination began, on the brink of getting knocked out and then won 7 consecutive games to lift the Cup, won 2 more WCs without dropping a single game both times obliterating the other 2 Asian sides in the final.