Wenger saw his 22-year spell with Arsenal come to an end during the summer, but the latter half of his reign was blighted by protests against his management and a lack of major silverware.
Ferguson and Wenger were involved in one of the most notorious rivalries of the Premier League era in charge of United and Arsenal respectively before later enjoying a more amicable relationship, and Baptista believes that the Frenchman can consider himself on a par with his long-time adversary.
"I don't think [Wenger] stayed too long [at Arsenal]. I can put Arsene Wenger on the same level as Ferguson," Baptista told Sports Mole at FIFA's The Best awards.
"Wenger spent the past  years at Arsenal; it's so difficult. You don't spend so many years at one club if you're not a very very good coach and a very good manager.
"In the history of Arsenal he's helped to bring them up, he brings new talent, creates great players and this I can say for his  years at Arsenal."
Wenger won four Premier League titles and a record seven FA Cups during his time in charge of the Gunners.