Aaron Barry's goal appeared to have earned they Candystripes all three points until the dramatic intervention of Limerick sub Chiedozie Ogbene.
Derry took the lead when Barry's header put them ahead but they were denied by Ogbene's scrappy close-range finish.
The result leaves Derry in fourth place and 17 points behind leaders Cork City.
Limerick went into the game without a win in their last five outings and looking to bounce back from a 3-0 away defeat to Sligo Rovers last time out.
A win for the home side would have put them level on points with Derry but the Candystripes have now strengthened their bid for European qualification and are four points behind Dundalk in third place.
City manager Kenny Shiels made one significant change from the side that lined out in Galway on Monday night with midfielder Nicky Low returning at the expense of defender Ben Doherty as the visitors started with a three-man back line.
Limerick made a bright start and Derry captain Gerard Doherty had to make a superb double-save in the 18th minute when he blocked Dean Clarke's effort before pushing Shane Duggan's shot over the bar.
Home keeper Brendan Clarke also had to scramble to save a powerful shot from Aaron McEneff before denying the follow-up by Nathan Boyle with his legs.
Neither side could create many clear cut chances at the start of the second half with Clarke wasting a free header for the hosts when his effort flew over.
The double substitution of Mark Timlin and Mikhail Kennedy in place of Josh Daniels and Nathan Boyle turned the game back in Derry's favour as Limerick started to tire.
After a period of sustained pressure, McEneff's corner found Barry at the near post and the defender's powerful header flew past Clarke to break the deadlock.
Derry appeared to be comfortably defending their lead until a frantic finish to the game with Ogbene scrambling the ball home in the 93rd minute.
Limerick: B Clarke; Kelly, Williams, Whitehead, Robson; O'Conor, Lynch, Duggan (c), Tosi, D. Clarke, Mulhall. Substitues: Hall, O'Flynn, Turner, Ogbene, Kenny, Cotter, Hery.
Derry City: Doherty (c); McDermott, Barry, Jarvis; McEneff, McNamee, Monaghan, Low, Daniels, Curtis; Boyle. Subtitutes: Grimes, Holden, Timlin, Doherty, Todd, Whiteside, Kennedy.
Derry City were held to another draw away from home after a last minute equaliser earned Limerick a 1-1 draw at Markets Field.