Burton had defender Nathan Stanton sent off for a second yellow card 15 minutes from the end but rarely looked like surrendering a 2-0 lead given to them by top scorer Calvin Zola and midfielder Lee Bell.
Burton boss Rowett said: "Our effort and work-rate was first class and I thought we created some good opportunities against a team that hasn't conceded an awful lot of goals in the course of a fantastic run of results.
"We've proved again that when we're on our mettle and do the right things, we're capable of causing anyone problems.
"Even at 10 men we limited them to very, very few chances which shows what a great group of players we've got."
But Rowett was less than complimentary about Stanton after the defender was given his marching orders for his part in an off-the-ball spat with Southend defender Luke Prosser.
The Burton boss said: "It was stupid of someone with his experience to get involved.
"The first booking I found difficult to understand, but he still shouldn't have got involved in something that gave the referee the chance to send him off."