The Italian outfit failed to win a race in 2014 and recently appointed Maurizio Arrivabene as their new team principal after sacking Marco Mattiacci.
There has also been a change in the car with four-time world champion Sebastian Vettel replacing Fernando Alonso.
Marchionne said: "2015 will be a difficult year that will put the team to a real test."
The Fiat Chrysler chief executive, who replaced Luca di Montezemolo as Ferrari chairman in October, continued: "I think 2015 is going to be a reconstitution year. It will be Maurizio's first full year with the team.
"I think hopefully within the next 12 months we will remove all the baggage of uncertainty that is going to plague at least the initial phase of 2015."
Ferrari came fourth in the constructors championship in 2014, behind Mercedes, Red Bull and Williams.
Marchionne added that his team, whose engine has been outperformed by champions Mercedes, were paying a price for decisions made under the previous management.
"We started late with the 2015 car, certain choices and strategies that were made by others and that, in retrospect, I don't necessarily share," said the 62-year-old Italian.
However, with Vettel replacing Alonso, who has rejoined McLaren, and work under way on improving their car, Marchionne is confident they can recover ground on their rivals by the end of 2015, in particular Mercedes.
"Some of the work has already started," he said. "We need to be able to emulate their success."
Arrivabene said he would consider two race wins next year a success, adding: "If we win four, we go to heaven."
Ferrari chairman Sergio Marchionne has warned that 2015 promises to be another testing year for the Formula 1 team.