The Brazilian, who moved to the Saudi Pro League side from Paris St Germain in the summer for 90 million euros ($94.23 million), was on target in an incident-filled clash that saw both teams reduced to 10 men with seven minutes remaining in the first half.
Aleksandar Mitrovic had headed the Saudi outfit in front in the 18th minute before referee Ma Ning sent off Al Hilal's Salman Al Faraj and Nassaji's Amir Houshmand after consulting the pitchside monitor following an on-field melee.
Neymar doubled Al Hilal's lead with a perfectly timed left-foot strike in the 58th minute and substitute Saleh Al Shehri put the seal on a comfortable win in injury time.
The victory was Al Hilal's first in the group phase of the continental competition this season after the four-time champions started their campaign with a draw against Navbahor last month.
The Uzbek side backed up that result with a 3-0 win over Mumbai City on Tuesday to join Al Hilal on top of Group D with four points after goals from Jamshid Iskanderov, Jasurbek Yakhshiboev and Doniyor Abdumannopov secured victory.
Al Ain from the United Arab Emirates took the top spot in Group A with a 4-2 win over Turkmenistan's Ahal as Uzbek outfit Pakhtakor slipped to a 2-0 loss against Al Fateh from Saudi Arabia.
Al Ain backed up their opening-round win over Pakhtakor with an impressive attacking performance in front of their own fans as Brazilian midfielder Erik put the former champions ahead in the fourth minute with a clinical finish.
Soufiane Rahimi and Kodjo Laba ensured Al Ain had a three-goal lead at the break and, while Elman Tagayew pulled one back in the 58th minute, Kouame Kouadio netted a fourth for the hosts that meant Dayanch Meredow's late strike was only a consolation.
Al Ain now have a three-point cushion over Ahal and Al Feiha, who had a goal in each half from Abdelhamid Sabiri to thank for their 2-0 win at home over Pakhtakor.
The winners in each of the 10 four-team groups are guaranteed to progress to the last 16, with the remaining places filled by the three teams from the east and west of the continent with the best runners-up records.
