With Norwich City in action at home to Hull City on Wednesday, Marcelo Bielsa's men knew they had the chance to take top spot.
And they wasted no time at the Madejski Stadium, Mateusz Klich getting them up and running with the opener in the 14th minute.
Luke Ayling created that goal and the right-back was soon at it again, setting up Hernandez for the first of his brace.
And when Hernandez added his second of the game just before half-time, Leeds was heading into top spot with nine games to go.
Meanwhile, Bristol City moved into sixth spot, replacing Derby County, despite Lee Johnson's men failing to beat bottom side Ipswich Town at home, Lloyd Kelly scoring an own goal to hand the Tractor Boys a point.
Ipswich is 11 points adrift of safety with Paul Lambert's side now having drawn five of their past six Championship fixtures by the same 1-1 scoreline.
Sheffield United moved within a point of Norwich thanks to its 2-0 win at home to Brentford despite Gary Madine's first-half red card.
Captain Oliver Norwood converted a penalty to put the Blades in front before Madine was dismissed, David McGoldrick striking late to seal the points.
Sheffield Wednesday's unbeaten run under new manager Steve Bruce continued with a 2-0 win away to crisis club Bolton Wanderers.
Steven Fletcher and Rolando Aarons struck either side of half-time to send the Owls up to ninth in the table, just three points outside the play-off places.
Wigan Athletic remains two points above the relegation zone after a crushing 3-0 defeat away to Blackburn Rovers, Danny Graham netting a brace at Ewood Park.