Bonaventura had originally been left on the sidelines for Friday's clash in Split but joins the squad two days after striker Simone Zaza and defender Andrea Barzagli were sent home due to lack of fitness.
It emerged later on Tuesday that Juventus 'keeper Gianluigi Buffon (elbow) and Paris Saint Germain midfielder Marco Verratti (left calf) could miss Friday's clash due to injury.
"Both are under observation although both will remain with the squad," said Italy team doctor Enrico Castellacci.
"We will evaluate the condition of both players in the coming days, because we have two matches and so we will see who can play and when. All other players are match fit."
Zaza had already complained of a sore back prior to travelling to Italy's training camp at Coverciano, and Barzagli, who only returned to training last week after suffering an injury knock, has not fully recovered from playing a full 90 minutes in the Champions League final against Barcelona last Saturday.
Barzagli had already been replaced by Sassuolo defender Francesco Acerbi while Bonaventura's versatility up front gives Conte options against a side which held the Italians to a 1-1 draw at the San Siro last November.
"We're working hard so we can produce a solid performance," said Conte.
"They (Croatia) are a very strong side and showed that against us at the San Siro but we're fully focused on sealing our place in the championships."
Italy, second in Group H two points behind Croatia, face Niko Kovac's side at the Poljud stadium looking for their fourth win in five qualifying matches.
A win for Croatia would see them pull five points ahead of Italy and leave Conte's men in danger of being overtaken by Norway, who are only two points adrift ahead of their home game against Azerbaijan.
Conte, who led Juventus to three consecutive league titles before quitting to take charge of Italy, admitted he is considering other options to his trademark 3-5-2 formation.
"I have to find the best system to suit the players I have. The 3-5-2 is a good formation but we need to have alternatives for the future," he added.
Conte on Monday praised the achievements of his successor at Juventus, Massimiliano Allegri - who led Juve to the Champions League final, and a 3-1 defeat to Barcelona.
But he launched a plea to ageing midfield maestro Andrea Pirlo, who some reports have linked with a move to a team in the Major Soccer League (MLS).
"I'm really happy Andrea still wants to continue," said Conte.
"He hasn't told me anything, but knowing him I'm sure he is still as passionate and enthusiastic for the national side.
"I don't believe he is thinking about international retirement, or of leaving Italy."
Italy, who lost the Euro 2012 final to Spain, will follow Friday's qualifier with a friendly against Portugal in Geneva on Tuesday.