Goals from Ivan Perisic and Antonio Candreva inside the first 15 minutes at San Siro ensured the spoils in a game that was halted late on by disruptive fans.
Some supporters threw flares onto the playing surface with little under 20 minutes to play, causing a brief delay.
Conte claimed Niko Kovac's men were better prepared for their Euro 2016 qualifier, and was consequently thrilled to stay level with Croatia on 10 points through four games.
"It's a step forward. It wasn't easy and the [Manuel] Pasqual injury didn't help, so we gave [Roberto] Soriano his debut," Conte told Rai Sport.
"Let's say this game against a team that is in better shape, has been together for a long time, with more experience and great quality, was tough.
"This team has the desire to improve and fight for every ball. We can improve, of course, but the hunger is there.
"I also thank the fans for coming to San Siro in such numbers."
Conte had made all three of his substitutions by the 63rd minute, with defender Pasqual, and strikers Ciro Immobile and Simone Zaza all making way.
The former Juve boss said his side had to adapt to the changes.
"Due to the injuries we had to make do, so switched to four at the back," he said.
"It's inevitable in the second half we lost our usual reference points and moves, but the lads wanted to bring home a positive result."
The men he brought on, Soriano, Stephan El Shaarawy and Graziano Pelle all impressed, and Conte hailed his side's depth.
"It's important, as we need everyone, from El Sharaawy to Pelle, Soriano and [Andrea] Bertolacci," he said.
"We need these new faces who can bring fresh enthusiasm and desire to the squad."
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