Substitute Rickie Lambert bundled the ball over the line deep into stoppage time after a poor attempted clearance by Ashley Williams to settle a match of little consequence at either end of the table.
And Monk believes that his side - already assured of Premier League survival heading into Saturday's fixture - defended well for the most part against his former club, but let themselves down in the dying seconds at the Liberty Stadium.
"Losing the game in the last minute is always hard to take," he said. "We suffered in the first half possession-wise playing against a very good team in Southampton.
"They worked their shape well, they worked their possession well, but we had three clear-cut chances that we should have scored from.
"I can't actually remember Michel Vorm making a save the whole game. We had the best chances - how we came away from that game with nothing is hard to take.
"It's been the story of our season. Very good defending for 90 minutes and then we let ourselves down with some schoolboy defending.
"We left ourselves open for the sucker punch."
Chico Flores had been expected to make his return from suspension, but Monk revealed that the Spanish defender "declared himself out of the squad" with a cut toe.
