Rafter instead included Nick Kyrgios and Thanasi Kokkinakis in the squad to join veteran Lleyton Hewitt and doubles specialist Chris Guccione for the January 31-Feb 2. tie.
Jordan Thompson would be the travelling reserve.
"It's going to be a fantastic environment for these kids, and good for us as well," Rafter told reporters at Melbourne Park of his decision to include 18-year-old Kyrgios, Kokkinakis (17) and Thompson (19).
"It's at that stage where you want to believe and make this team as strong as we can and as deep as we can.
"I like the idea we got obviously Bernie there ready to come back after his operation, and Marinko hopefully able to overcome the things he needs to overcome to become a great Davis Cup player."
Rafter said dropping Matosevic, who had been in the top-40 last year, was a decision that had been tough to make but he felt it would aid the 28-year-old in the long run.
"Marinko understands. He knows what he has to do. Even though Marinko is the number two player, he's still learning, I guess, all the time," Rafter said.
"He came on the scene a little bit later than most of the guys do, and certainly with the two 'Ks' (Kyrgios and Kokkinakis) he's a lot later.
"So he's still learning his way, how he fits in the whole scheme, on the tour as well.
"We believe by having him out at this stage it will help him to be more hungry. He is hungry. He wants to be back on the team, and that's exactly what we want to see from him."
Australia will face a French team laden with top-ranked talent with world number nine Richard Gasquet and number 10 Jo-Wilfried Tsonga available for the matches on clay in La Roche sur Yon.
(Writing by Greg Stutchbury; Editing by Patrick Johnston)
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