The Tigers lock gained his ninth cap in Scotland's 27-3 defeat by the Springboks. South Africa scored three tries in seven minutes in the period leading up to half-time.
After Chris Paterson had kicked a penalty to put Scotland ahead, the visitors struck back with two Percy Montgomery penalties and converted tries from Bryan Habana, Jaque Fourie and Fourie du Preez.
Hamilton was replaced by Scott Murray after 48 minutes as coach Frank Hadden took a last look at his squad before the World Cup.
Scotland: Lamont, Walker, Dewey, Henderson (Southwell), Webster; Paterson (Parks), Blair (Lawson); Kerr (Jacobsen), Ford (Thomson), Murray, Hines, Hamilton (Murray), White (captain), Callam (Hogg), Brown.
South Africa: Montgomery; J P Pietersen (Willemse), Fourie, Steyn (Pretorius), Habana; James, du Preez (Pienaar); du Randt (B J Botha), G Botha (du Plessis), van der Linde, B Botha (van den Berg), Matfield (captain), Burger, Rossouw (van Heerden), Smith.