The Azzurri required only a point from their third and final group-stage fixture to secure a top-two finish in Group B and progress to the last 16, but they were made to work for that point against a Croatia outfit that needed to win to reach the knockout rounds.
After deploying a 4-3-3 formation in Italy's first two group games, Spalletti opted to take a more pragmatic approach to the beginning of their encounter with Croatia and switched to a 3-5-2 system.
However, the European Championship holders struggled to get going during an uneventful first half before going behind 10 minutes after the break when Luka Modric fired home from close range, just 33 seconds after having a penalty saved by Gianluigi Donnarumma.
Spalletti soon ripped up the 3-5-2 system and made a host of attacking changes in the closing stages in search of an equaliser, while Croatia themselves switched to a five-at-the-back system as they attempted to see out the victory.
Spalletti insists Italy were "not prudent" in Croatia draw
Italy's persistence in the final third eventually told and they scored a dramatic 98th-minute equaliser with the last kick of the match from substitute Mattia Zaccagni, who curled a stunning first-time strike into the top corner to spark wild scenes among the Azzurri.
The result means Italy have qualified as runners-up in Group B, setting up a last-16 clash with Switzerland at the Olympiastadion in Berlin on Saturday, while third-placed Croatia are on the brink of elimination.
Speaking to the media after the match, Italy boss Spalletti defended his tactics and insisted that his side's struggles were not down to the system deployed on the night.
Asked by Sky Sports Italia if his team were too prudent in their initial approach to the match with a 3-5-2 system, Spalletti said: "We were absolutely not prudent. If the limitation is that we struggle to play out from the back with simple balls, then we will struggle with any lineup or any tactical system that we use.
"In the first half, we lost the ball in ways we absolutely cannot afford to do. That's not prudence. If we don't play with quality, if we do the basics and nothing more, then we will struggle.
"It was not about the system, we were too timid in the first half, but the system was irrelevant compared to the attitude and quality seen on the field."
Spalletti laments "really banal errors" in Croatia draw
Spalletti added: "There's no denying it, we were below our usual level in the first half. If we don't create very much, we're not going to score very much.
"You can see we were thinking about bringing a result home, without really believing that we needed a win. It was involuntary, but I expect more from my players, because they show it in flashes.
"They do have the quality, but at times we make really banal errors. We have better capabilities than what we saw today.
"Jorginho played well today, so did [Nicolo] Barella, [Riccardo] Calafiori is a top player who knows how to do everything. We have ways of playing out from the back, but we've got to do better."
Italy, who have now failed to win any of their nine meetings with Croatia (D6 L3), have five days to rest and prepare themselves for their last-16 clash with Switzerland, who finished as runners-up in Group A behind Euro 2024 hosts Germany.
One Azzurri star who will not be available for selection against the Swiss in defender Calafiori, who will serve a one-match ban due to an accumulation of yellow cards.