Victor Moses's first league goal for the Blues had looked set to secure an away victory at the Liberty Stadium on Saturday before Hernandez continued the Swans' recent resurgence under Michael Laudrup with a superb strike.
Chelsea have claimed just a point from their last two league matches after defeat by Manchester United last weekend.
They now trail new leaders United by a point following the Red Devils' 2-1 win against Arsenal at Old Trafford earlier on Saturday.
Although the match lacked the controversy of last weekend's contest, John Obi Mikel was booed by some sections of the crowd in the early stages.
This appeared to be a nod to the Blues' decision to lodge a formal complaint with the Football Association over allegations Mark Clattenburg used "inappropriate language" towards the Nigeria midfielder during the United match -- an allegation the referee denies.
The visitors were almost caught off guard as early as the third minute when Angel Rangel was threaded through down the right channel only for Branislav Ivanovic to make a last ditch interception to cut out his cross to Michu.
Laudrup's team had Leon Britton to thank when he hooked a Fernando Torres header off the line in the 12th minute.
But soon afterwards the hosts threatened again when Hernandez's clipped ball dissected the Blues defence, however Michu was unable to divert goalwards with his outstretched boot.
Moses, man of the match in the thrilling 5-4 midweek League Cup win over United, looked lively again and Torres could only head tamely into Gerhard Tremmel's hands after the Swans goalkeeper had parried the Nigeria international's cross into the Spaniard's path.
Mikel came to Chelsea's rescue with a fine block to deny Ki Sung-Yueng after he was teed up by Wayne Routledge, while shortly before half-time Ashley Williams foiled a swift Blues counter-attack when he did well to prevent Torres squaring to the advancing Eden Hazard.
Although clear-cut chances had been at a premium, it had been an even and entertaining first half, yet the European champions, who replaced Oriol Romeu with Ramires upon resumption, then increased their grip on proceedings.
Tremmel excelled by tipping a Hazard free-kick around his post but, from the resulting corner, Chelsea got their goal.
Oscar's pinpoint set=piece was headed goalwards by Gary Cahill and Moses, inside the six-yard area, executed a sublime headed flick which flew in off the underside of the crossbar.
It was only Moses's second goal since his pre-season arrival from Wigan, the other having come against Wolves in the League Cup, and he received a standing ovation from Chelsea fans when replaced by Daniel Sturridge in the 72nd minute.
Incessant hailstones made the conditions difficult for both sides and Chelsea keeper Petr Cech was almost caught out by Swans substitute Nathan Dyer's audacious chip with 75 minutes gone.
It looked as though the Blues had done enough to escape with all three points, yet Hernandez had other ideas as he exchanged passes with substitute Itay Schechter before driving a low shot into the bottom-right corner which escaped Cech's reach.