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Martin Demichelis scored the opener in the 77th minute, while Martin Palermo doubled the lead second a minute from time.
In the second match of the group, South Korea recorded a 2-2 draw that allowed the Asian side to reach the last 16 as runners-up in Group B.
The South Koreans fell behind to Kalu Uche’s 12th minute opener, but recovered strongly courtesy of Lee-Jung Soo’s 38th minute effort and a Park Chu-Young free-kick on 49 minutes. Nigeria equalised when Yakubu rolled in a penalty on 69 minutes.