Albion top-scorer Maupay - who cost £20million from the Bees in August 2019 - lashed an unstoppable effort into the top right corner just before half-time to light up a below-capacity Amex Stadium.
Leandro Trossard set the Seagulls on course for a first top-flight success in more than three months with an instinctive 34th-minute volley.
Brentford had second-half opportunities to salvage something but were denied by a couple of superb saves from Brighton goalkeeper Robert Sanchez, while Marc Cucurella brilliantly cleared an Ethan Pinnock header off the line.
Victory for Graham Potter's hosts ended a barren streak stretching back to a 2-1 success over Leicester on September 19, lifting them to ninth in the table.
Belgium international Trossard made the initial breakthrough, expertly guiding a deft, first-time finish over the advancing Fernandez following Enock Mwepu's perfectly weighted ball over the top.
Brentford were seeking consecutive Premier League wins for first time and soon had a mountain to climb courtesy of a former hero.
Maupay - who scored 41 goals in 95 games during two seasons in west London - collected the ball from Jakub Moder before unleashing an unstoppable drive beyond Fernandez from just inside the D.
The stunning finish was Maupay's seventh strike of the season and third in as many appearances after he rescued late points at West Ham and Southampton at the start of the month.