Argyle, unbeaten in six in all competitions ahead of Tuesday's FA Cup replay at home to Port Vale, took a 65th minute lead through midfielder Dominic Blizzard's 20-yard drive, which took a deflection off Michael Timlin.
Southend replied two minutes later as danger man Kevan Hurst latched on to a through ball from substitute Cauley Woodrow to claim his 10th goal of the season.
Plymouth central defender Curtis Nelson then hit the post with a shot in stoppage time.
"It was a fair result," Brown said. "Both sides came into this in a good vein of form, I was looking at this as difficult fixture.
"Plymouth have got some rhythm now and something going for them. John has got a striker scoring goals in (Reuben) Reid and there is a positive feel down here.
"We had to match them in terms of workrate and although we were playing different systems we did seem to cancel each other out at times.
"It looked like our spare man in midfield was surplus to requirements, so we made the change and went 4-4-2.
"I thought the first goal might be the winning goal. Consequently when they scored it pricked the consciences of our players and we started playing well again.
"We got our equalising goal and saw the game out comfortably, although they hit the post.
"There were opportunities for both sides but I think both managers would say that a draw is a decent result."