South Korea had to fight to the last minute for the point which put them through after Greece were beaten 2-0 by Argentina.
Nigeria created chances throughout and took the lead when Chidi Odiah squared for Kalu Uche to tap in after just 12 minutes. But South Korea hit back through Lee Jung-Soo, who scrambled the ball past Vincent Enyeama from Ki Sung-Yeung's free-kick to equalise before half time.
Park Chu-Young's curled free-kick restored South Korea's lead four minutes into the second half but Yakubu coolly slotted in a penalty after Kim Nam-Il fouled Chinedu Obasi Ogbuke to level the game.
A frantic final 20 minutes ensued as both sides missed chances but the draw was enough for South Korea to progress.
Group B Final Standings
Group B W D L F A GD Pts Argentina 3-0-0 7:1 +6 9 South Korea 1-1-1 5:6 -1 4 Greece 1-0-2 2:5 -3 3 Nigeria 0-1-2 3:5 -2 1