The Brazilians went down to strikes by Siyabonga Nkosi and Kingston Nkatha at FNB Stadium, with Clayton Daniels's ricocheting effort forcing a consolation own goal by Amakhosi skipper Itumeleng Khune.
Neeskens said afterwards, "We did it to ourselves. In the first half we controlled the game. We had more of the possession but then after (the break) Chiefs were winning all the second balls, the 50/50s. We gave them all the time."
The Dutchman added, "We have to look ahead but first I will watch the game again and analyse it."
Downs, who outclassed Chiefs 4-1 in the MTN8 quarter-finals, next visit Moroka Swallows in the last-four of the competition on Sunday. The teams drew their first leg duel 3-3 in Tshwane this past weekend.