Trailing 2-0 with 15 minutes left, the Czechs looked headed towards a second Group D defeat with Croatia on track for a last 16 spot after goals by Ivan Perisic and Ivan Rakitic.
But a fine 76th minute glancing header from fellow substitute Milan Skoda cut the deficit before trouble broke out as flares rained down and Croatia fans fought each other.
After the mayhem, a handball by Croatia's Domagoj Vida left Necid, who had come on only three minutes earlier, to coolly put away his spot kick to level the scores.
"I told my players at halftime that if they did not feel like playing we should not have come here," Czech coach Pavel Vrba said. "After the break it was much better. Now we have our fate in our hands."
The Croats, on four points from two matches, have themselves and their fans to blame after a largely one-sided encounter, as they appeared distracted by the disturbances at the end.
"Many Croatian patriots are ashamed in front of all of Europe, including our players who wear the shirt with so much pride and passion," said Croatia coach Ante Cacic.
"We played a good match and dominated. We had many chances but credit to the Czechs who made the most of their chances."
The Czechs earned their first point to stay alive in a group that also includes European champions Spain, who beat the Czechs 1-0 in their first game and were facing Turkey later on Friday with their opponents having lost 1-0 to Croatia in their opener.
STRUGGLING CZECHS
The Czechs struggled for most of Friday's match, dropping deep as the Croats, with captain Darijo Srna in the lineup after his father's funeral, immediately taking control.
Srna, in tears when the national anthem played, managed to get his emotions under control as he implemented his side's gameplan which stifled the Czechs for most of the game.
Croatia threatened early on through Perisic who wasted an opportunity, but he quickly made amends for his miss, pouncing on a Czech error and beating goalkeeper Petr Cech with a well-placed low drive into the far corner in the 37th minute.
Croatia, promised beers by Cacic if they won, were soon rewarded again with Rakitic slipping into the box and timing his chip perfectly to beat Cech and make it 2-0.
However, instead of finishing off the game by finishing any of several more good chances, they allowed their opponents to stage a comeback.
Croatia playmaker Luka Modric had to go off with a thigh muscle injury on the hour and that changed the balance of the game.
Skoda's header gave the Czechs a glimmer of hope before the game was interrupted as flares and other objects landed on the pitch behind riot police deployed in front of the Croatia fans.
This was followed by fighting among the Croatian supporters as referee Mark Clattenburg took the players towards the centre of the pitch and consulted an official.
When they game resumed Croatia were punished for a lack of concentration, conceding the penalty which led to the equaliser from Necid that keeps the Czechs' qualification hopes alive.
(Reporting by Karolos Grohmann, Additional reporting by Zoran Milosavljevic; Editing by Ken Ferris)
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