The Belgian finished 4.9 seconds ahead of Evans to take a provisional 18 points in the championship battle, while the Welshman earned 15 points after an eight-stage battle where the gap between the two never exceeded five seconds.
Eight-time world champion and part-time Toyota driver Sebastien Ogier (40) completed the top three 11.6 seconds off the top spot, with the Frenchman earning 13 points going into the Zagreb-based rally's final round on Sunday.
"It's not a big lead, but we had a great day. Despite a not-perfect tyre choice this afternoon we were capable of defending our lead," said Neuville.
"We need to continue attacking and have a good tyre choice on Sunday. It wasn’t easy when the weather wasn’t very easy to judge."
Estonian Ott Tanak (36) was fourth, a minute and 15.5 seconds further back to claim 10 points ahead of Frenchman Adrien Fourmaux’s (28) Ford Puma in fifth.
Sunday's four-stage finale completes the 54.78 km in the Croatian capital with 12 championship points still up for grabs.
