Robin Bormuth had given the hosts a first-half lead before Christoffer Nyman levelled after the hour-mark and Hernandez struck with a minute of normal time remaining.
The hosts were buoyed by their first win of 2017 last weekend and Friedhelm Funkel was even happier to welcome Kaan Ayhan back in for youngster, Emmanuel Iyoha.
Braunschweig and Torsten Lieberknecht also made just the one change after drawing with Stuttgart last Monday as Maximilian Sauer replaced the injured Phil Ofosu-Ayeh.
Fortuna on top, Bormuth gets the goal
Fortuna clearly still had plenty of confidence after their late win over Bochum and began the match on the front foot. Within the first 30 seconds, good work from Ihlas Bebou saw Oliver Fink and Ayhan both have strong shots well blocked by the brave Braunschweig defence.
However, things soon turned and a clear through ball from Nyman saw Suleiman Abdullahi race through on goal. However, and thankfully for Fortuna, Michael Rensing was able to half his one-on-one attempt before doing similar with his follow-up from a tighter angle.
As things calmed ever so slightly in a frantic game, Marcel Correia was forced off with injury. That meant Joseph Baffo was given an early entry into the game than he perhaps expected. Play progressed and there were chances at either end. Hendrick Zuck's curler was blocked by Kevin Akpoguma, while Fink failed to catch a volley cleanly.
Ayhan's presence on Fortuna - despite the victory against Bochum - was clear to see just how important he is to the side. This time, a curling free-kick was tipped wide.
Set-pieces would prove to be the way to the opening goal, although this time it was Rouwen Hennings' delivery that caused the panic. His curling cross from deep deflected off Ken Reichel's shoulder before dropping to Marcel Sobottka. He was brilliantly denied by the busy Jasmin Fejzic before Bormuth bundled the ball home from close range.
Braunschweig bounce back
The second half began in the same vein as the first ended. Fortuna should have been two up as well, as Bebou deflected Lukas Schmitz's superb delivery in with his shin but the linesman had wrongly flagged for offside. The hosts continued to come forward and a clever pass from Sobottka ended with Fejzic's clawing over Hennings' lobbed volley.
Yet Braunschweig did not lose heart and pushed themselves for an equaliser, which another well-worked move between their front two provided. A long ball forward was headed into the air by Nyman before dropping to Abdullahi. The Nigerian took the ball into the box before Nyman swept the ball expertly into the far corner from 14 yards.
The pace of the clash was incredible and eventually saw more fouls creep in as the two teams began to tire. That still didn't stop them from moving to try and find a winner, as Fink's snapshot was well-held at the near post by Fejzic before Rensing made a similarly important stop to cut out Hernandez's cross towards Nyman.
Iyoha was introduced with five minutes left and the 19-year-old had an immediate impact, as his turn and run and header seemed to bring new life to his team. Yet it wouldn't be Fortuna celebrating a late winner. Hernandez's late effort from long range looked comfortable for Rensing but a deflection off Akpoguma's head instead took it into the far corner.
The action didn't stop there, as Julius Biada set up Domi Kumbela at the death who hit the post and had the ball cleared off the line. At the other end, the final kick off the game saw Bebou go on a mazy run before striking the outside of the post with the outside of his boot as the Lions took all three points.
It was a game that could, and perhaps should have finished level given the disallowed goal. Braunschweig bunched up the top four as a result, while Fortuna sit 10th.