The winger crossed for three of his team's 10 tries to match New Zealand legend Jonah Lomu's all-time milestone of 15 overall at the tournament.
The Springboks will next face the loser of Saturday's match between the top two Pool A teams, Australia and Wales.
The winner of that game will take on either Scotland or Japan in the last eight. The Scots can clinch second place by beating Samoa on Saturday in Newcastle, ahead of the closing match between Japan and the U.S. on Sunday.
In the other game Wednesday, Namibia narrowly lost to Georgia 16-17 at Sandy Park in Exeter. Namibia face Argentina on Sunday, but do not have a chance of advancing beyond the pool stage. The African side, the lowest ranked in the tournament, has never won a World Cup match.
Georgia's win, their second in the competition, all but guarantees the side a place in the 2019 World Cup, due to take place in Japan.
"Georgia came along to the World Cup for the first time in 2003, and now in 2015 we're in the top 12 teams at the World Cup," said prop Davit Zirakashvili after playing his last game for the side.
"It's really something beautiful for a small country like Georgia. I hope in the coming years that we will climb to the top 12, top 10 or top eight."
The Americans have yet to register a point from three games, though managed to hold the two-time world champion Boks to just 14-0 at halftime.
However, Heyneke Meyer's team then ran in eight tries after the break, with Habana notching his hat-trick in the space of just 19 minutes.
It was the biggest winning margin of the tournament so far, and the American Eagles' largest World Cup defeat.
In the company of a legend
Rugby superstar Lomu scored seven tries at his first World Cup in 1995, including four in the semifinal victory over England, but New Zealand lost to host South Africa in the title match.
The giant winger ran in another eight tries at the 1999 tournament hosted by Wales, with two coming in the All Blacks' semifinal defeat by France.
Habana made his World Cup debut in 2007, when he matched Lomu's record of eight tries at a single tournament and helped the Springboks win the title.
He crossed twice at the 2011 event, when South Africa lost in the quarterfinals.
The 32-year-old went tryless as South Africa suffered a shock 34-32 defeat against Japan in the team's 2015 group opener, but scored once each against Samoa and Scotland before Wednesday's treble.
He could have had four in the match, but spilled the ball when he dived over the tryline in the 68th minute.
Habana now has 64 tries at international level, equal the total of former Australia star David Campese -- the most by a any player among the top-tier nations. Japan's Daisuke Ohata has the overall record of 69.