But Brighton remain in third on goal difference and face tricky games against Derby at home and Middlesbrough at the Riverside on the final day.
Following pre-match protests the game was halted after just 30 seconds as Charlton supporters threw balloons and beach balls onto the pitch in protest at Duchatelet’s ownership of the club.
Similar protests occurred at the start of the second half, while the game was also halted for a short time in the 89th minute after a flare was thrown onto the field.
Had the Seagulls scored two more goals they would have gone up into second place on goal difference – and they had enough chances after the break to do it.
Baldock shot wide from a tight angle after a good ball from Baram Kayal, before forcing a great save from Nick Pope while Hemed nodded a great chance wide and Anthony Knockaert’s late curling effort forced Pope into another great save.
But they had to make do with Skalak’s excellent strike into the top corner and Hemed’s spot-kick, which came after Rod Fanni chopped down Knockaert in the area in stoppage time.
Brighton manager Chris Hughton:
“It’s a wonderful position to be in and one we would not have expected to be at this stage of the season.
“To be where we are is a credit to the group of lads. I think once you get to this stage the pressure is equal on each of the teams. We are all desperate to get promotion in whatever way that is.
“We’ve made the goal difference tighter there’s no doubt about that. We have scored the goals at the right time. We certainly deserve to be in there with the two other teams.”
Charlton manager Jose Riga:
“This is not the first time we have faced this situation. We had the same game against Middlesbrough. We had to be very ready, we were not. The players of Brighton were ready but I don’t want any excuse, we know the context.
“The players gave their all and competed. We had a good reaction in the second half and equalised.
“Of course I’d prefer another atmosphere than this one.
“Communication will not be enough. It’s about acting and showing some decisions now.
“We have to learn from our mistakes. It happens, relegation. We can build something. You see the story of Bournemouth. That is an inspiration for us and a lot of teams.”