Trailing 4-1 in the third set, Safina swept the next four games to claw her way back before finishing off the 91st-ranked Pin with a forehand winner to end the two hour 36 minute battle.
Pin, who has played just one match win since Barcelona in June, had the 14th-ranked Russian in deep trouble with back-to-back breaks in the third set but could not deliver the knockout punch.
"I think I can say, I'm not one who will give an easy match," Safina told reporters. "I always try to fight for every point, especially when you don't feel like 100 percent.
"Then there is no other way, just shut up and fight."
Safina's victory completed a perfect day for the seeded players with all six in action advancing to the second round.
Patty Schnyder continued her impressive buildup to the U.S. Open with a 6-3 6-2 win over Spain's Anabel Medina Garrigues.
The 10th-seeded Swiss struggled in the gusty conditions before prevailing in a sloppy opening set that featured five breaks. She seized command with an early break in the second and sent her Spanish opponent to a first-round exit for the third consecutive year.
Schnyder has enjoyed a solid start to the hard court campaign, reaching the quarter-finals in Cincinnati and Stanford before falling to Maria Sharapova in three sets in the San Diego final.
Twelfth seed Tatiana Golovin of France advanced with a routine 6-2 6-1 victory over Ukraine's Julia Vakulenko but Israel's Shahar Peer had a tougher passage, the 11th seed battling past Dutchwoman Michaella Krajicek 7-5 7-6.
Slovenia's Katarina Srebotnik was also made to work for her place in the second round, the 14th seed dropping the first set before roaring back to register a 5-7 6-2 6-2 victory.
Czech 16th seed Lucie Safarova also needed three sets to dispose of Uzbekistan's Varvara Lepchenko 6-4 6-7 6-1.
The Toronto Cup has been hit hard by the late withdrawals of Sharapova, Venus Williams, Amelie Mauresmo and Martina Hingis but the $1.3 million event still boasts four of the world's top five players led by number one Justine Henin.
The Belgian, who received a first round bye, returns to the court in Toronto for the first time since her semi-final loss to Frenchwoman Marion Bartoli at Wimbledon.
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