The 33-year-old, widely considered the best player in the history of the women's game, slammed home from the spot in the 74th minute against Group C winners Italy to secure qualification and take her World Cup tally to 17 after Debinha was bundled over by Elena Linari.
That puts her one ahead of former Bayern Munich and Lazio striker Miroslav Klose in the all-time rankings, and the veteran attacker said the goal was more than just a personal triumph.
"The feeling is a joyful one, definitely, not only for breaking the record but for being able to represent women in doing so," she said.
"And for being able to help my team which is what matters most, qualifying for the next stage of the tournament."
Marta's record-breaking spot-kick wasn't enough to secure second place in the group however, as Sam Kerr's incredible four-goal haul in Australia's 4-1 hammering of Jamaica saw the Matildas leapfrog Brazil on goals scored as three sides finished on six points.
It means they could face either France or Germany in the next round, a tough test for a team that has at times spluttered in the group stage.
"I think that when you play a big competition like a World Cup, you can't choose who you play," insisted Marta.
"We have this thing now, we need to do what we need to do to keep this thing going in the competition and then whoever we have to play we will be prepared."
The Aussies will play Norway in Nice in the next round on Saturday after they made sure of qualification on Monday with a scrappy 2-1 win over eliminated South Korea that came thanks to two penalties.
Having lost their opening match with Italy they looked dead and buried as they headed towards half-time against Brazil two goals down, but clawed back to win 3-2 before comfortably seeing off the Jamaicans, who finish the group stage with no points to their name despite Havana Solaun scoring the Reggae Girlz' first ever World Cup goal four minutes after the break.
Kerr became the first Australian woman to score a World Cup hat-trick when she tapped home in th 69th minute following two first half headers, and her fourth was the goal that secured second spot.
Italy meanwhile will take on one of the four best third-placed finishers after topping the group ahead of Australia on goal difference, while Brazil have to wait to know their opponent.
"It's hard to think of such a thing as a 'good defeat', but you could say that we're happy for qualifying and finishing first in the group," said Italy coach Milena Bertolini.
England take centre stage on Wednesday as they attempt to match Italy in finishing first in Group D when they take on Japan, while Argentina look to squeeze into the next round when they take on bottom side Scotland.