The USA clinched first place in Group A when Sweden defeated North Korea, 2-1, in the other group finale. The Americans face England in the quarterfinals on Saturday at Tianjin's Olympic Center Stadium (TV: ESPN, live, 7:55 a.m. ET).
North Korea, which went into Tuesday's play tied with the USA for first place, claimed second place ahead of Sweden on goal difference and will meet Germany on Saturday in Wuhan (TV, ESPN2, live, 4:55 a.m. ET).
"I am also very proud of my players because this is a very difficult group," said U.S. coach Greg Ryan. "Tonight's games allow us to go first in our group, which was an important goal for our team. To go through without a loss in this group, I'm very, very happy that we've reached this stage."
The win extended the USA's unbeaten streak to 50 games -- 49 since Ryan took charge of the national team in 2005 -- and kept its unbeaten record in Women's World Cup group play intact at 15 games (13 wins and two ties, against China in 1995 and North Korea in 2007).
Center forward Abby Wambach, who scored the first goal in the USA's 2-2 tie with North Korea and scored both goals in the 2-0 win over Sweden, was again at the heart of the U.S. attack.
The goal came on a set piece when Wambach flicked Cat Whitehill's throw-in toward the six-yard box on to Chalupny, who took it down with her chest and toe-poked a shot that took a deflection off a Nigerian defender's leg and into the lower left corner for her fifth career international goal. It was also the second fastest goal at the beginning of a match in Women's World Cup history.
For the second time in three games, the encounter was marred by wet weather. Sheets of rain fell during the entire game, making the field was soft and slippery.
Nigeria's best chance of the game came in the 75th minute when Perpetua Nkwocha got a step on Whitehill into the right side of the penalty box, but slid her shot wide left of the goal as U.S. goalkeeper Hope Solo came out to challenge.
Ten minutes later, the Falcons again came close, but Solo made a point-blank save on Rita Chikwelu's shot.
The result was a far cry from the 7-1 and 5-0 victories over Nigeria at the last two Women's World Cups.
"One of the great things about football is that it's played in all sorts of weather," said Ryan. "You have to adjust and adapt to the conditions. I think that we could have played better possession tonight. I feel like we gave the ball away too easily. We played passes too strong in the wet conditions and too far in front of players in the first half. I thought that in the second half maybe we settled down and played a little bit better. But the field conditions were difficult for both teams, and again I am very impressed with the skillful play of the Nigerians, their ability to settle the ball and play attractive soccer."
In the other Group B match, Lotta Schelin's two goals gave Sweden its victory over North Korea. The results meant that the USA avoided a quarterfinal showdown with Germany.
The Yanks have won six of nine games against England (with two losses in 1985 -- their first year of play -- and 1988 and a 1-1 tie in 2007).
Sept. 18 in Shanghai
USA 1 Nigeria 0. Goal: Chalupny 1.
USA -- Solo, Rampone (Ellertson, 77), Markgraf, Whitehill, Lopez, Boxx, Chalupny, Lloyd (Osborne, 64), O'Reilly, Wambach, Lilly.
Nigeria -- Dede, George, Ikidi, Jerome, Cole, Ekpo, Mbachu, Chikwelu, Igbo (Chiejine, 22), Nkwocha, Uwak (Chukwudi, 83).
Yellow card: USA -- Cole 14.
Referee: Mayumi Oiwa (Japan).
Shots: USA 16, Nigeria 10
Shots on goal: USA 6, Nigeria 2
Saves: USA 2, Nigeria 5
Corner kicks: USA 4, Nigeria 1
Fouls: USA 10, Nigeria 19
Offside: USA 0, Nigeria 3