The Argentina captain saw his spot-kick saved in the opening stages, denying the defending champions what would have been a first-half equaliser.
Instead, Egypt carried a one-goal advantage into the interval and stretched it to 2-0 in the 67th minute, leaving Argentina on the brink of elimination.
The fightback gathered momentum when Cristian Romero reduced the deficit before Messi delivered the crucial equaliser in the 83rd minute.
The strike, his tournament-leading eighth goal, sparked wild celebrations as he sprinted to the corner flag, jumped twice into the air, pumped his fist and pointed towards Argentina’s travelling supporters.
Argentina completed the remarkable comeback in stoppage time when Enzo Fernandez headed home the winner, securing a dramatic 3-2 victory after trailing by two goals.
Messi later reflected that fate had intervened during Argentina’s recovery from a seemingly hopeless position. After the final whistle, the emotional captain broke down in tears as teammates gathered around him to celebrate another memorable escape.
The squad then carried Messi onto their shoulders and tossed him into the air in the middle of the pitch before embracing following a victory that kept Argentina’s World Cup title defence alive.
Read: Egypt Coach Accuses Officials of Favouring Argentina After World Cup Heartbreak
“The truth is that it was a moment of release, a release for all of us,” Messi said.
“I was feeling intense anger because of the penalty I wasted, and because of the way I took it. I felt like in that important moment, I had let the team down.
“But fortunately, God had something special in store for me once again in the end, and I was able to score the equaliser.
“That was a huge release, and immense joy for us, and for those fans who came again and prove every day what it means to be Argentine, and how much pride they give us.”