Tom Pett and Jobi McAnuff went close for Boro in the opening 10 minutes, before the visitors took the lead on 21 minutes through a coolly taken penalty.
After soaking up plenty of Southend pressure as the half progressed, Stevenage equalised three minutes before the break when Rowan Liburd headed home after Dean Wells headed Jobi McAnuff's corner back across goal.
Wells and his trialist centre-back partner both saw headers saved from consecutive corners in the second half and Boro looked the more likely to score, but instead they were grateful for a fine late save from Chris Day to emerge with a draw.
McAnuff, Wells and Liburd were among six players who got 90 minutes under their belt as competition continues to hot up for first team places ahead of Saturday's trip to Portsmouth.
Stevenage: Day, Kerr, Wells, Trialist (O'Keefe 77), Fox, Guerfi (Brady 35), Tonge (Dowridge 72), McAnuff, Pett (Wilmot 88), McKee (Cregan 46), Liburd