Totti, 34, now has 206 goals, which is one more than Baggio managed during his playing career from 1986 to 2004.
"I compliment Totti because many can score 100 goals but to pass the 200 mark, few achieve that," said Baggio.
"Totti has fought so much and has won each challenge.
"He has given everything, putting in love on and off the pitch.
"For all that he has achieved, he deserves all this satisfaction.
"He merits all the applause."
Totti made his Serie A debut in 1993 at the age of 16 and has spent his entire career with Roma, his hometown club.
There was speculation that Totti could retire earlier this season after a poor start to the campaign.
However, the former
"He, like others that suffer setbacks, has been doubted, but through courage and pride, he has emerged," said Baggio.
"I tell Totti not to give up, to continue and to focus on the next record because he has the strength and the condition to score many more goals."