Leeds ground three points out of a game that turned on a 55th-minute red card shown to Josh Brownhill as Hernandez and Roofe struck late on to draw a line under the club’s heaviest defeat of the season.
Brownhill incurred a second yellow card for a foul on Roofe, allowing United to take control of a match which had been meandering until then.
City struggled to cope with United’s pressure and were cut open as Roofe turned home a chance from close range on 69 minutes and Hernandez converted an 88th-minute header.
An injury crisis had forced Bielsa to field two academy debutants - goalkeeper Will Huffer and centre-back Aapo Halme - but Bristol City failed to force a single save of note from 20-year-old Huffer.
Johnson, however, claimed the red card had denied his players a potential victory, saying: “We were looking like the side who were going to go on and win the game at that point.
“It was potentially a bit of naivety from Josh, a player who should be experienced enough to deal with that.
“I thought they (Leeds) were lucky. They got away with it. Sometimes when your luck’s in your luck’s in, and that showed today.”
Bielsa, whose team lost 4-1 at West Bromwich Albion in their previous game, said: “It’s a point of view that we have to respect but we should analyse the argument used to reach this conclusion.
“I could say that we virtually didn't concede any chances. I don't know any situation that we suffered so for me it's difficult for me to think that we deserved to lose the game.
"But I always take into account other points of view. When I see the game again I'll take into account this point of view - that we didn't deserve to win the game.
“At the beginning of the second half and from minutes 25 to 35, we didn't dominate. For the rest of the time we dominated. The fact that we played with one player more made it easy for us but I don’t think it was the only argument.”
Huffer, an England Under-20 international, was handed his first debut after senior keepers Jamal Blackman and Bailey Peacock-Farrell were lost to injury ahead of Bristol City’s visit.
Halme, meanwhile, stepped into replace Pontus Jansson in a makeshift defence which also featured midfielder Kalvin Phillips.
“Aapo Halme, inside of a defensive structure which prevented any danger, gave a good performance,” said Bielsa, whose squad climbed to second place in the Championship at full-time.
“For Will it’s different because he didn't have to go through a challenge. The main difficulty for him was to assimilate the pressure as it was his first game.”