Earlier, Liverpool skipper Steven Gerrard had given his team the lead with a free-kick in the 65th minute as the hosts looked to be on course for yet another derby win.
But Jagielka’s magnificent 91st minute strike was enough for the Toffees to spoil Liverpool’s party and keep the Reds in search for their third Premier League win of the season.
Liverpool manager Brendan Rodgers was obviously left deflated by the outcome of the game and the manner of the result.
“We didn’t get what we deserved,” said Rodgers.
“I never felt in any danger during the game. I think the organisation of the players was very good. They had good concentration. I always felt that with the ball we were a real threat going forward. But when you conceded so late on like that, into injury-time, it’s a little bit frustrating.”
The game began at a frenzied pace and referee Martin Atkinson could have given away two penalties and a red card within the opening 10 minutes.
Everton midfielder Gareth Barry had a boiling start to the game after being booked inside the first minute and then nearly gave away a penalty a few minutes later after Alberto Moreno’s shot struck his raised hand in the middle of the penalty area.
Adam Lallana went closest to breaking the deadlock with a header onto Raheem Sterling’s cross but Tim Howard made a fine save to deny the former Southampton man’s first goal for his new club.
Howard remained the busier keeper in the first-half having to make further saves onto efforts from Jordan Henderson and Raheem Sterling to keep the visitors afloat.
Meanwhile Everton lost their marauding winger Kevin Mirallas to a hamstring injury on the half-hour mark and had to be replaced by Aiden Mcgeady.
Liverpool resumed their onslaught in the second-half but could not make any real headway past a dogged Everton defence until Leighton Baines brought down Mario Balotelli a few yards outside the penalty box.
Steven Gerrard stepped up for the resultant free-kick to curl it into Howard’s far side and this time the American keeper was beaten despite getting his fingertips.
A couple of minutes later Howard made a fine save from close range to deny Balotelli’s first time effort from Sterling’s cross.
Despite being unable to add to their advantage Liverpool looked in prime position to finish the game off and collect the three points.
But in the first minute of stoppage-time Phil Jagielka struck an unstoppable thunderbolt on the half-volley from 25 yards which flew off the crossbar into the far top-corner of Simon Mignolet’s goal.
Both Liverpool and Everton have endured slow starts to the season and the shared points on derby day means that both the Merseyside clubs will remain adjacent in league table on 13th and 14th positions respectively.