Despite scoring from the spot against West Brom three days earlier, Fernandes let Rashford take the penalty that made it 3-0 after the England forward had been sent flying by Boli Bolingoli.
Bayern Munich turned the game around as ex-Gunner Serge Gnabry hooked in an equaliser before England captain Harry Kane scored a penalty after William Saliba fouled Leroy Sane.
The England midfielder then netted an injury-time volley to continue his fairytale start to his Real career. Bellingham, 20, now has 14 goals in 16 matches for club and country this season.
The England midfielder now has 12 goals in 15 matches for club and country this season. Alvaro Djalo pulled a goal back for Braga but Real held on in Group C.
West Ham had 20 shots and might have equalised just before Garnacho's first had Emerson Palmieri capitalised on an error by Harry Maguire on the England defender's return to the team.
Belgium, England's Group G opponents, were again without injured defender Vincent Kompany in Brussels, while Eden Hazard limped off in the 70th minute.
"This match was so important to build the momentum again," England winger Saka told TNT Sports. "Going out of the FA Cup really hurt me so I'm sure we'll use that to push in the Premier League and the Champions League next month.
England forward Rashford made it 2-0 with a 20-yard finish before Jesse Lingard's deflected shot found the net. Anthony Martial added the fourth from a Rashford assist, Lloyd Dyer scoring a stoppage-time consolation.
The England forward said during pre-season that he welcomes the added competition up front following the arrival of club record signing Alexandre Lacazette .
The England international made the most of an under-hit back pass from Marouane Fellaini, rounding David de Gea and rolling the ball into an unguarded net.
Walcott had scored a hat-trick at the same Maksimir Stadium for England against Croatia in 2008 but, despite pulling one back, he could not repeat such heroics.
City, needing three points to become champions of England for the seventh time, took the lead just before half-time through Raheem Sterling's close-range strike.
The Meji Alabi-directed video was shot across continents, with scenes filmed in London, England - Eazi's home base for much of 2020 - and at Balvin's HQ in Colombia.