Lynagh, the Australian captain, was attempting to prove his fitness after damaging a thigh muscle six weeks ago, when he suffered a recurrence of the injury during the second half of Queensland's 24-22 defeat by Western Samoa at Ballymore yesterday.
There was better news for the centre Jason Little, who was recalled after knee surgery. The front row forward Phil Kearns will captain the team in Lynagh's absence.
It was the third win in a row on the tour for Western Samoa, who had to overcome a 16-6 deficit at half-time and the dismissal of one of their try-scorers, the second row forward Mata'afa Keenan, for stamping.
New Zealand have recalled the lock Ian Jones for the third and final Test against South Africa in Auckland on Saturday. Jones, who returns after injuring his cheekbone in the first Test in Dunedin, replaces Mark Cooksley in the only change from the side that beat South Africa 13-9 a week ago to take a 2-0 lead in the series.
South Africa enjoyed a 21-11 victory over Canterbury at Lancaster Park on Saturday. Japie Mulder scored two tries for South Africa, and Andre Joubert hit three penalties and a conversion. Mark Mayerhofler scored a try for Canterbury and Andrew Mehrtens landed two penalties.
AUSTRALIA (Test v Western Samoa, Sydney, 6 August): M Pini; D Smith, J Little, P Howard, D Campese; D Knox, G Gregan; T Gavin, D Wilson, W Ofahengaue, G Morgan, J Eales, E McKenzie, P Kearns (capt), T Daly.
NEW ZEALAND (third Test v South Africa, Auckland, 6 August): S Howarth; J Kirwan, F Bunce, J Timu, A Ieremia; S Bachop, G Bachop; Z Brooke, M Brewer, B Larsen, I Jones, R Brooke, O Brown, S Fitzpatrick, R Loe.Reuse content