The Stags celebrated their first win on home soil in 12 attempts stretching back to September, Sam Clucas and James Jennings on target.
Southend were unbeaten in their previous eight but had substitute Conor Clifford sent off nine minutes from time for diving in on Matt Rhead, before grabbing a last-gasp consolation through Ryan Leonard on an afternoon of gusting gales and heavy downpours.
"Conditions were difficult, but I was disappointed with the decisions by the officials which were nothing to do with the conditions," Brown said. "It was almost like there was a conspiracy theory going on against us.
"We had a couple of penalty appeals turned down and the red card for Conor Clifford was a disgrace.
"I am not here to berate officials and I am not blaming them for the result as we were not good enough.
"But I was two or three yards away from the incident and the fourth official was only a yard away and he told us no way was it a red card.
"So why did he not translate that to the referee who came rushing over to show a red card?
"They are told to bide their time before they make decisions. For me it was a very inexperienced decision, though it hasn't cost us the game.
"Conor got the ball and came out with the ball and didn't use excessive force.
"Also the corner Mansfield scored from wasn't a corner to start with but, Sod's law, it comes in and it's in the back of our net.
"But we were the reason we got beat, though if we'd had a slice of luck we could have won it comfortably."
- Sports & Recreation
- Conor Clifford
- Matt Rhead
- Ryan Leonard