United arrived on the South coast pumped up by last weeks 2-1 Worthington Cup semi final first leg win over Liverpool.
But it was Portsmouth who started the better with defenders Matthew Taylor and Hayden Foxe both wasting clear openings inside the first ten minutes.
Taylor should have done better when played through by Steve Stone after five minutes, but shot straight at United goalkeeper Paddy Kenny.
Australian international Foxe wasted an even better chance five minutes later when he placed a header wide of the post after Gianluca Festa had flicked Paul Merson's cross into his path.
Pompey were made to pay for their misses midway through the first half when busy United striker Peter Ndlovu opened the scoring.
The former Coventry frontman played a neat one-two with highly rated midfielder Michael Tonge before sending a deflected shot past Pompey keeper Shaka Hislop from ten yards out.
But the vocal home fans did not have to wait long to cheer the equaliser with Merson's midfield partner Gary O'Neil making it 1-1 three minutes later.
O'Neil, Pompey's best player on a frustrating night for the league leaders, calmly chipped in his third of the season from six yards after on-loan Stathis Tavlaridis had prodded the ball into his path.
But it was Brown who had the last word, just as the home fans were celebrating a deserved point, as he seized on a mistake by Foxe and fired the winner past Hislop from ten yards out.
Portsmouth: Hislop, Stone, Primus, Foxe, Festa, Taylor, O'Neil, Quashie, Merson, Todorov, Pericard. Subs: Kawaguchi, Diabate, Tavlaridis, Harper, Burton.
Sheff Utd: Kenny, Jagielka, Murphy, Page, Quinn, Montgomery, Brown, McCall, Ndlovu, Tonge, Allison. Subs: Kozluk, Ten Heuvel, Kabba, Smith, Peschisolido.
Referee: C Wilkes (Gloucestershire)