Ndala fired home from the spot on 71 minutes in Jakarta after the Samba Boys had gone into a two-goal lead thanks to efforts from Kaua Elias on 43 minutes and Da Mata on 54 minutes.
The result wasn’t decisive through as the Three Lions still progressed to the knockout stages as group leaders after victories over New Caledonia and Iran in Matchday One and Two.
England will now take on the best third-placed team from Group A, B or F on Wednesday, kick-off 08:30 (UK).
In the game itself, Warhurst could have opened the scoring on 20 minutes as he fired a crashing volley off the bar while Ndala came close himself when he curled a clever effort just wide moments later after being set up by fellow blue, Oboavwoduo.
Warhurst again nearly had his name on the scoresheet in the 26th minute but his pinpoint header was expertly kept out by Brazil stopper Gabriel, with Oboavwoduo setting him up with a wonderful cross into his path.
Elias fired Brazil ahead with a intelligent volley on 43 minutes and they doubled their advantage on 54 minutes with a Da Mata header.
City forward Ndala got England back into it with a penalty that had to be checked by VAR on 71.
After being confirmed by the review system, Ndala – fouled to earn the spot-kick in the first place – stepped up and made no mistake.
Ryan Garry’s youngsters eyed a leveller but it didn’t come with both sides coming close before the final whistle blew.