The Marlins had remained confident throughout the process a deal would be reached, and by the deadline, Peters agreed to a bonus of $175,000.
Peters was projected to be taken in the top three rounds, but in May, he sustained a torn ligament in his throwing elbow, which required Tommy John surgery.
The Marlins had 12 total selections in the first 10 rounds of the Draft, and all are under contract.
In all, the Marlins reached agreements with 33 of their 42 selections. Miami, which also signed two undrafted free agents, reached agreements with its first 22 picks.
"You can call this Draft a success in terms of just the amount of players we signed with the Top 20, but I think we also got some athletic players," said Marlins vice president of scouting Stan Meek. "We got some athletic players up the middle that really addressed a need for us. Also, in addition to the second overall pick in Tyler Kolek, a big right-hander, we also got a good group of college left-handed pitchers that we feel add a lot of depth to the system.
"We feel good about the guys we signed, we're excited."
The headliner of Miami's class is the hard-throwing Kolek, a prep sensation from Shepherd, Texas. The 18-year-old signed shortly after being taken for $6 million, and he has already made four starts for the Gulf Coast League Marlins, for whom he is 0-2 with a 4.50 ERA in 10 innings.
Kolek's fastball was clocked as high as 102 mph in high school. He has 10 strikeouts thus far in his 10 frames.
Some of the early-round picks already impressing in the Gulf Coast League are speedy second baseman/shortstop Justin Twine (second-rounder), shortstop Brian Schales (fourth-rounder) and outfielder Stone Garrett (eighth-rounder).
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter