Rhodes, back from scoring two goals in five games for Rochdale, continued his good form scoring one in each half.
The first was a clinical finish just before the break after a Dean Bowdwitch pass.
Lokando, just back from a month's loan with Dagenham & Redbridge, handed Rhodes his second from the spot when he brought down Bowditch in the box on 57 minutes and was sent off for his troubles.
As the game entered it's last quarter Joyce made a good save from Danny Haynes but then Southend started to show at last why they've had such a good start to the season with their first extended period of pressure.
The wonderfully named Shane Supple in the Town goal had to pull off three oustanding saves to preserve the Ipswich lead and he did enough to give them the points.
There will be a quick chance for the United players to get this out of their system as the club have arranged another behind closed doors friendly next week, there's not another league fixture for nearly a month, this time at the Tottenham Hotspur training ground.
Southend United Reserves: Joyce, Lokando, Jones, Herd, Reynolds, Scannell, McCormack, Grant, Forshaw (Abbey 60), Walker, Laurent.
Unused subs: Masters, Ademeno, MacDonald, Osifawa.