Brown looked on in despair as mistakes from Isaac Osbourne and Jamie Langfield gifted Saints two goals before further sloppy play led to the clincher at McDiarmid Park.
The defeat was all the tougher for Brown following on from an impressive display against Hibernian at the weekend.
Brown said: "It was a poor performance. How we can go from being excellent at the weekend to playing poorly in the last period of the game was unaccountable.
"Each goal was a gift. The first goal we conceded was alarmingly softly but St Johnstone took their chances."
Meanwhile, the Dons manager confirmed the club were hoping to sign Czech goalkeeper Dan Twardzik after Jason Brown left Pittodrie on Tuesday.