Olivier Giroud put Chelsea in front only for Daniel Podence to level. Neto thought he had earned an 81st-minute penalty but referee Stuart Attwell agreed with the VAR that Reece James had made no contact with the Wolves forward. But Neto still proved to be the hero as he slotted home deep into added time.
It was a cagey first half with few openings, but Chelsea did carve out two excellent opportunities.
Giroud had a great chance in the 19th minute from Ben Chilwell's corner, but he headed over when unmarked six yards out.
And in the last minute of the first-half, Kurt Zouma was unlucky not to find the back of the net when he headed onto the bar from a Mason Mount corner, with Giroud unable to react quickly enough to put the loose ball away.
Wolves' best chance was a speculative Neto effort from outside the area which Edouard Mendy comfortably pushed behind.
Chelsea had to wait only four minutes of the second half to break the deadlock, and Giroud continued his good run of form. Chilwell produced a great cross from the left which Giroud turned towards goal first time and Rui Patricio couldn't hold. The goalkeeper made a desperate attempt to claw the ball out but Attwell pointed to his goalline technology watch to indicate the ball had crossed the line.
Fabio Silva thought he had scored his first Premier League goal to put Wolves level six minutes later but the flag went up for offside.
The equaliser did come in the 66th minute when Thiago Silva's attempted headed clearance fell to Podence, and he showed neat footwork before firing past Mendy via a deflection off James.
Wolves thought they had a penalty nine minutes from time when Neto went down inside the box when James attempted to make a challenge, but there was no contact and Attwell correctly reversed his decision after the VAR advised he look again at the pitchside monitor.
But Wolves did win it with just 10 seconds of added time remaining, breaking from a Chelsea attack and Neto showed great composure to slot past Mendy and earn the victory.
There was time for Neto to almost add a third, but Mendy kept him out.
"At 1-0 we should see the game out," said Chelsea boss Frank Lampard, who suggested his team may have become complacent after their 17-match unbeaten run before defeat at Everton on Saturday. "If you are not playing that well, which we weren't at that time, hang on to 1-0, don't allow counter-attacks," he said.
"Performance is what gives you results. We were playing very well, a long unbeaten run and then maybe the lads think we are playing well and the minute you think you are playing well things like this can happen."