Hornchurch suffered a 2-0 defeat to league rivals Bowers & Pitsea while Wingate & Finchley lost 3-0 to Corinthian Casuals.
Second-half strikes from Danny Norton and Bradley Sach meant the injury-hit Urchins missed out on the chance to host Aldershot Town in the fourth qualifying round of the FA Cup.
Both sides played out a goalless first-half with chances being created at both ends.
In the 54th minute Danny Norton opened the scoring for the visitors before they then doubled their lead with 10 minutes left to play as Sach tapped home a Dan Trendall cross.
Hornchurch will now look to bounce back when they return to league action on Saturday away to East Thurrock United.
League rivals Wingate & Finchley suffered a 3-0 defeat at home to Corinthian Casuals.
Goals from Warren Mfula, Elliott Bolton and Bobby Mills sealed the progress of the Casuals which sees them take on St Albans City in the next round.
Mfula opened the scoring in the eighth minute and they took that lead into the half-time break.
Elliott Bolton and Bobby Mills had both netted to make it 3-0 within three minutes of the restart.
The visitors then cruised to victory.
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