Midfielder Jones lobbed Brighton goalkeeper Casper Ankergren from 20 yards in the third minute of time added on after the Dane had made a mess of an attempted clearance.
All the goals came in the second half and the Seagulls broke the deadlock two minutes after the break when former Rochdale striker Glenn Murray showed awareness to head home after his initial header from Elliott Bennett's free-kick had rebounded off the crossbar.
Dale drew level six minutes later through Jones' penalty after Brighton skipper Gordon Greer was shown a straight red card for punching substitute Rochdale Anthony Elding, who would only come onto the field moments later.
Former Wolves winger Bennett looked to have put Brighton on the way to their second successive victory when he scored with a tremendous 20-yard shot in the 67th minute.
But Rochdale pushed hard in the closing stages and came close through Chris O'Grady and Elding before Jones struck to give them a deserved point.