"I have tremendous respect for his baseball mind and know he'll make a great addition to Michael's team," owner Jeffrey Loria said in a statement.
Hill, who has been with the team 11 seasons, entered the game 20 years ago, when he was drafted by the Rangers.
"He has ascended quickly through the ranks, thankfully with us for more than a decade," Loria said in the statement. "Michael is an amazing guy who has earned this well-deserved recognition."
The Marlins on Friday dismissed Larry Beinfest as president of baseball operations. The club also let go of Jim Fleming, who was a special assistant to the president of baseball operations.
Titles aside, Hill made it clear that the front office will be working as a team.
Hill and Jennings have a long history together, each coming up in the Tampa Bay system.
Jennings recalls the days when Hill worked out of a closet, and the two of them staying up to 2 a.m. at times putting together a plan to build a Minor League system.
"We will work together," Hill said. "I'm the senior-most person in baseball operations, but we don't do anything here by ourselves. We will work together to make sure we do everything to win as many games as we possibly can."
Loria met with Hill for more than an hour on Friday to discuss the future. Jennings had been out of the country, scouting in Venezuela, until Friday night. He was at Marlins Park on Saturday, watching the Marlins' 2-1 victory over the Tigers in 10 innings.
Per the statement, there will be no further changes to the senior executive team.
"It has always been our policy not to communicate publicly about people's careers until final decisions have been reached," Loria said. "For that reason, I wanted to wait until the end of the season to make these announcements. I hope this statement clarifies the situation and allows us to get back to the important work of improving our team for the 2014 season."
Jennings has developed a close friendship with Loria through the years, and he thanked him for all he's done for himself and his family.
"Let me say this, and I'd like to put this out there," Jennings said. "There has been no one in this game that has treated me better than Jeffrey Loria. My family and myself, he's taken care of us. He's been giving. He's given advice. He's taken care of me and my family financially."
Hill added that Loria has always been part of the decision-making process, and that will remain the same.
"This is a question we've been asked a lot," Hill said. "He's a part of the process. It's part of my job and Dan's job and the people we work with to formulate the plan. That will be how we move forward. As any owner, he has the right to ask questions, and we try to educate him on whatever it is we want to do. I don't think that's any different from how things operate anywhere else.
"From that standpoint, we're good. We've spent a lot of time the past few days talking about everything, because his goal -- as is everyone else's goal -- is to return to excellence."
With the Marlins wrapping up their fourth straight losing season, carrying a 61-100 record into the contest with the Tigers, Hill spoke about a new beginning.
The franchise has enjoyed success in the past with limited resources. They were World Series champions in 2003, and enjoyed winning seasons from 2003 to 2009.
"The first thing we're going to do is re-evaluate where we are and formulate a plan that puts us in position where we go, 'OK, we have these things as our strengths, we have these things coming that can help us soon,'" Jennings said. "What we're going to have to do is assess what our weaknesses are."
Because the Marlins aren't expected to dramatically raise payroll for 2014 -- it will stay roughly $37 million -- they may be looking to deal some of their young talent to bring in missing pieces.
Perhaps the biggest asset the Marlins have is slugger Giancarlo Stanton, who will be entering arbitration for the first time.
The Marlins are planning to build around Stanton, but it is unclear if they will be able to sign the slugger to a long-term contract.
"The big man is a big part of our future," Hill said. "D.J. started to discuss some of the challenges that we face as we move forward. The pieces, as we have said, we feel some of them are here who will help us return to our glory and win a championship here.
"It is our job to surround those people with more talent. That's what we need to do. We need to get better, plain and simple. We need to get better. It's sort of interesting that the season is ending today, because we're just getting started. ... We need to focus on getting better and winning more games, and Giancarlo is going to be part of that."
Upgrading an offense that ranks last in the Majors in runs, batting average and home runs is going to be a priority.
"I think we're going to try to change a few things. We're looking at a 100-loss season," Hill said. "We need to get better. Bottom line is, we need to win more ballgames. I think the future is bright here.
"We knew this year was a season of transition. People who have had an opportunity to see this team play, they see the talent. They see the young pitching, the position players. We do have work that we need to do, because we aren't where we want to be. We don't want to lose 100 games. We want to get better. The process starts today to make things better."