Neuville beat teammate Esapekka Lappi by 33 seconds after the final day's four stages, with Toyota's championship leader Kalle Rovanpera finishing a distant third and the Finn's teammate Elfyn Evans fourth.
Rovanpera leads Neuville by 25 points after six of 13 rounds, with Kenya's Safari Rally next up on June 22-25.
"We came here with the belief that we could fight for victory but the first day was challenging and we lost a bit of time," said Neuville.
"It's the first victory for the team this year, it's a one-two, and the first time for our team principal (Cyril Abiteboul) as well. Craig (Breen) is in our memories as well. We wanted the win in Croatia but we got it now."
Hyundai's Irish driver Breen died in a crash during testing for the Croatian round in April.
The win was the 18th of Neuville's career.
