Nigeria started the game top of the group but the 0-0 draw allowed co-hosts Australia to move up to first place after they thrashed Canada 4-0.
Nigeria's pay dispute has overshadowed their campaign, with the outspoken Waldrum saying he was owed seven months' wages and some of his players had not been paid in two years.
However, the American coach said he was proud of what the African side had achieved despite the negatives.
"I just told them that two years ago, when we started this journey, so many things went well and so many things didn't go well. They never gave up, they continued to believe," a smiling Waldrum said after they sealed qualification for the last 16.
"You know, I was actually disappointed in the second half because we could have won the match. So it almost feels disappointing that we didn't get the result, the three points.
"But all of us would have taken this result before we started the match just to know we got through."
Nigeria will stay in Brisbane to play the winners of Group D, where England are in pole position with a three-point lead ahead of their final group game against China.
"If it's England, it's the European champions. We've already played the Olympic gold medallists (Canada). We've already played the host nation (Australia)," he said.
"So it's just going to be another one of those matches that we've already been playing in."
Ireland return home with their first-ever point at the World Cup and coach Vera Pauw said it was a "fantastic feeling" to draw against Nigeria, who she described as a top-10 nation despite the African side being ranked 40th in the world.
"They are the 11-time African champions and we had the better play. They always looked dangerous but we were in control, we created chances," Pauw said.
"I think we can be really proud. We played three top 10 nations, I think Nigeria are a top 10 nation, we have played equal games against them. We lost by penalty (against Australia), an own goal (against Canada) and now we draw.
"It's amazing, those players came into this tournament as very good players and they go out as world stars. It will change their lives, they will get other contracts and more opportunities and the next generation can step in."
