A pulsating game at the Proact ended 3-3 following an added time equaliser and penalty save by Spireites defender Will Evans.
Ebbsfleet went into half time 3-0 up after goals from Michael Cheek, Cody McDonald and Bagasan Graham.
However, an unlikely second-half comeback was started by Tom Denton and Marc-Antoine Fortune before Evans' 95th minute header.
Soon after, Callum Burton was sent-off following an off the ball incident, but Evans heroically saved Cheek's 99th minute penalty to earn John Pemberton's side an improbable draw.
The Spireites had the first chance of the game after just two minutes. Jonathan Smith lined up a shot from 25-yards, but his effort was straight at Nathan Ashmore.
The referee, Rebecca Welch, was not endearing herself to the home support after Lee Shaw was taken down with a rash challenge on the edge of the box, but she failed to signal for a free kick.
Six minutes later, Haydn Hollis was lucky to not see red after bringing down McDonald just outside of the Chesterfield penalty area. From the resulting free-kick, Jack Payne's effort rose well over Burton's crossbar.
On 22 minutes, the away side were awarded a dubious penalty when Burton was adjudged to have brought down Cheek down in the area.
The forward dusted himself down and sent Burton, who was yellow carded for the foul, the wrong way to score his ninth goal of this season.
Jamie Sharman was taken off after 35 minutes due to a twisted ankle and was replaced by Tom Denton.
Five minutes before the break, the Fleet made it 2-0. McDonald received the ball in the box before twisting and turning past Hollis and firing home into the bottom left corner of Burton's goal.
Two goals would soon become three in first half stoppage time, as Graham powerfully drove the ball into the back of the net.
At half time, Pemberton made another substitution as Alfie Beestin was replaced by Robbie Weir.
The first big chance of the second half fell to the hosts on the 51st minute, when Ashmore failed to claim the ball from a cross, but Shaw's goal bound effort was cleared off the line.
With 25 minutes of the game to go, Chesterfield reduced the deficit. Bradley Barry curled a brilliant cross onto the head of Denton, who headed past Ashmore from close range.
The goal suddenly woke both the players and fans up, and Marc-Antoine Fortune wasn't far off a second just four minutes later. Shaw managed to work the ball into the box, but the attacker failed to get the proper connection on the ball.
Hollis was inches away from getting another goal back with just under 15 minutes to go, as a corner was flicked on by Fortune to the defender, but his header was somehow palmed away by Ashmore.
Chesterfield grabbed a second on the 83rd minute. Denton's flick on found Fortune before the striker slotted past Ebbsfleet's keeper.
Tensions were running high during the six minutes of added time. Ashmore was getting more and more wound up by the Spireite fans, and was yellow carded for time wasting before having a verbal altercation with a section of the support.
His time-wasting was soon punished. Kyel Reid's floated cross was headed by Evans into the back of net, via the post.
A little pitch invasion and yet more bickering followed. Ashmore was once more in the centre of the controversy.
A number of allegations have been made since, including one of racial concern, CEO Graham Bean has said.
However, the equaliser wasn't the last moment of the game. Burton claimed the ball from a free-kick but he was soon in trouble after clashing with Cheek in an off-the-ball incident.
The goalkeeper on loan from Hull City was subsequently sent off and a second penalty of the game for Ebbsfleet was awarded.
Evans took up the role as goalkeeper and Cheek once more took on the responsibility of scoring from 12-yards. Remarkably, the defender guessed the right way and pushed the ball way from goal.
The final whistle sounded soon after to end an incredible afternoon at the Proact Stadium.
As much as the draw feels like a win, the point knocks Chesterfield down a place in the National League to 22nd.
Next up for the Spireites is Bedford United in the FA Trophy before a huge relegation clash away at Aldershot Town.
Post-Match Verdict: What a game!
Well, where do we start? Oh, the underwhelming first half. Ebbsfleet dominated play and fully deserved the lead. The referee in all fairness did make some dreadful decisions as well.
John Pemberton said: "Half time was interesting. I said a few things to them I felt they needed to hear and the response in the second half was absolutely unbelievable."
However, the second half was remarkable. Fantastic fight back from the team and added time was just madness.
The hero of the day Will Evans said: "The feeling of scoring the equaliser was incredible.
"Cal getting sent off and having to face a penalty was bizzare to say the least."
Of course, the allegations could cast a large shadow over the game but the club should most likely learn about that later in the next week.
Callum Burton's red card is definitely not a good thing. He now faces a three-game ban, which means we could have seen the last of the goalkeeper, unless his loan is extended.
This now, though, gives Joe Anyon and Shwan Jalal a chance to stake a claim as Chesterfield's number one.
Finally, it looks like John Sheridan will be appointed some time next week. There could be a few changes to make but he knows that he will have a squad that is willing to fight until the very end.