At the season's halfway point, United had to come from behind three times in a tumultuous, incident-filled match at Old Trafford before Hernandez buried the decisive goal.
"Once again they have proved their courage, never gave in — down three times and came back three times, and eventually deserved to win the game," United manager Alex Ferguson said.
"Never mind where we are at this moment in time, this was a championship performance."
As United bounced back from Sunday's draw at Swansea, City's three-match winning run came to an end after its former winger, Adam Johnson, gave Sunderland a 1-0 victory over the champions.
Chelsea is now only four points behind City with a game in hand after Juan Mata clinched a 1-0 victory at Norwich.
Tottenham, Everton and West Bromwich Albion are all two points behind Chelsea.
Tottenham moved into the fourth Champions League spot as Gareth Bale scored a second-half hat trick in a 4-0 rout of Aston Villa. Everton beat Wigan 2-1 and West Brom won by the same score at Queens Park Rangers, which sunk back to the bottom.
Reading moved ahead of QPR on goal difference by holding Swansea 0-0, while Southampton remained out the drop zone ahead of Wigan by drawing 1-1 at Fulham.
Newcastle looked like producing its first win at Old Trafford since 1972, but United's fighting spirit can rarely be supressed.
For the eighth time this season in the league, Alex Ferguson's players came from behind to win and keep a 20th English title in their sights.
But there will be lingering concerns about a defence that has now conceded 28 goals in 19 games, compared with 33 in the whole of last season.
United's defence was breached after just four minutes after Michael Carrick gave away possession inside his own half, and goalkeeper David De Gea then parried Demba Ba's strike only for James Perch to put Newcastle in front.
Evans levelled for United in the 25th, sliding the ball into an empty net after Hernandez's shot from Robin van Persie's free kick was only half-blocked by goalkeeper Tim Krul.
But Evans then scored at the other end three minutes later, inadvertently turning a shot from former United teammate Danny Simpson into the net.
The goal was initially disallowed but the referee's assistant because Papiss Cisse appeared to be offside, but the decision was over-ruled by referee Mike Dean.
Ferguson was furious, venting his frustration at fourth official Neil Swarbrick on the touchline, and then challenging Dean at the start of the second half.
But United pulled level again in the 58th, with Patrice Evra's low shot ending up in the bottom corner of the net.
Newcastle, though, was back in front 10 minutes later after Cisse latched onto a cross from former United winger Gabriel Obertan.
The lead didn't last long, with Van Persie netting his 16th goal of the season in all competitions in the 71st after seeing an initial shot saved.
Hernandez, who was playing due to Wayne Rooney's injury, was denied by Krul before finally connecting with Carrick's cross and sending a half-volley into the net.
While United recovered despite the best efforts of its former players in the Newcastle team, crosstown rival City was sunk by an old boy.
Johnson, who was offloaded in the off-season after winning the title with City, managed to leave Joe Hart red faced as his strike was deflected into the net by the goalkeeper in the 53rd.
"Last year we didn't win here and we won the title," City manager Roberto Mancini said. "It's important that our strikers start scoring more goals, sometimes we take one touch too many."
After hitting eight past Aston Villa on Sunday, there was a more routine victory for Chelsea at Carrow Road.
Juan Mata struck the game's only goal in the 38th after being fed by Oscar.
"Even without the ball he (Mata) is working hard but when we are in possession he is making the difference," Chelsea manager Rafa Benitez said.
Villa goalkeeper Brad Guzan, who conceded eight at Chelsea, was beaten another four times.
Jermain Defoe poked the ball through Guzan's legs in the 58th to put Tottenham in front after running onto Kyle Naughton's through ball.
Bale's first came four minutes later when he rounded Guzan and knocked the ball into the net.
The Wales winger was on target again when he slotted home from Aaron Lennon's pass, and he completed his treble in the 84th after being teed up by Gylfi Sigurdsson.
Everton also remains in the hunt for Champions League qualification after Leon Osman and Phil Jagielka netted in the second half against Wigan, which scored a late consolation through Arouna Kone.
West Brom also overcame a relegation-threatened side 2-1 to keep hot on the heels of Chelsea.
QPR goalkeeper Rob Green was beaten by Chris Brunt's long-range strike, and then turned the ball into his own net after a clearance from a corner looped off Armand Traore.
Djibril Cisse pulled one back from close range for QPR, which couldn't recover to prevent a second straight loss.
Liverpool's attempt to close in on the Champions League places stalled again after losing 3-1 at Stoke and dropping to 10th, eight points behind the top four.
Liverpool won a penalty after just 30 seconds when Luis Suarez was fouled by Ryan Shawcross, and Steven Gerrard converted from the spot.
But Stoke responded in the fifth minute when Jonathan Walters scored the first of two goals either side of Kenwyne Jones' header for the hosts, who rose above Liverpool into eighth.