Two excellent goals from defender Jordi Alba, one of eight Barcelona players in the starting lineup, and a fifth of the tournament from Fernando Torres gave Spain a third successive win and top spot in Group B.
They stretched their unbeaten run in competitive games to 28, going back to their 1-0 defeat to Switzerland at the 2010 World Cup, and have not lost at all since England beat them in a friendly in November 2011.
They will face Italy, who they beat 4-0 to win the European title in Kiev a year ago, at Fortaleza's Castelao in Thursday's semi-final.
"Nigeria were very dangerous in the first half and they played with plenty of dynamism and made it difficult for us," he told reporters.
"When it is as hot as it was today you cannot play like that for 90 minutes and Nigeria had to slow down.
"They were a bit less intense in the second half and we played better."
"We wasted a lot of chances. The players showed too much anxiety in front of goal. The good thing is we are creating a lot of chances, but we are not taking them. That is something we have to work on and hopefully it will come quickly.
"But we showed a lack of professionalism after we went 2-0 down and I was not happy about that, we lost our discipline."
Soldado had two good chances to increase Spain's advantage before the break but was twice thwarted by Nigeria keeper Vincent Enyeama.
Cesc Fabregas held his head in disbelief when he strode on to a cross from Soldado but, with only Enyeama to beat, shot against the post with the rebound flying straight into the goalkeeper's grasp.
