The Russian world number one, who has never won a Grand Slam but has lost three major finals, was down a break in the third set against the 167th-ranked wild card and looking fragile.
But Safina managed to stumble through an error-plagued contest lasting well over two and a half hours to eke out the win.
'It was a very tough one, but I made it into the second round,' she said. 'That's a positive thing because tomorrow is another day, another chance to step on the court and definitely play a better match.'
Safina squeezed through with 48 unforced errors to 65 for Rogowska, who made her New York debut.
'I'm disappointed that I was in a winning position and I let it go, but it's a great learning experience,' Rogowska said. 'I'm getting confidence that I can match it up to the number one player.'
Other seeds spared the drama with number four Elena Dementieva crushing Camille Pin 6-1, 6-2 and revitalised Serb number five Jelena Jankovic dispatching Italian Roberta Vinci 6-2, 6-3.
Number six Russian Svetlana Kuznetsova, a former champion, defeated German Julia Goerges 6-3, 6-2, and ninth-seeded Dane Caroline Wozniacki hammered Galina Voskoboeva of Kazakstan 6-4, 6-0, but Ukrainian Kateryna Bondarenko surprised 11th seed Anna Ivanovic 2-6, 6-3, 7-6 (9-7).
Maria Sharapova, the 2006 winner, continued her comeback from a shoulder injury with a solid 6-3, 6-0 dispatch of Bulgaria's Tsvetana Pironkova.
'I played a tricky opponent who doesn't give you much rhythm,' said the three-time Grand Slam champion Russian. 'It was just really important to stay on top of her and do the right things from the beginning.'