The Barcelona superstar joined Brazil's Neymar at the top of the World Cup scoring charts on four with a goal in the third minute and another, a superbly struck free kick, in first half stoppage time.
These came on top of his match-winning strikes against Bosnia-Hercegovina and Iran.
"Messi is one heck of a player, he's blessed," Keshi acknowledged after seeing his side lose but still qualify for the last 16 as runners-up in Group F.
Any chance Messi had of a hat-trick were dashed when coach, Alejandro Sabella, replaced him with Ricardo Alvarez after an hour.
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"It seemed to me at 3-2 that we needed Messi to rest - it was agreed beforehand," explained Sabella.
Messi, who enjoyed friendly banter with Nigerian keeper Vincent Enyeama during the game, said he was just happy he and his teammates had achieved their objective of qualifying.
"We hope to continue like this, I think today you saw a better Argentina," he said.