The hosts took a 1-0 lead ten minutes into the friendly at Earlsmead when trialist Dean Green scored from the penalty spot.
Blues levelled ten minutes into the second period through Jordan Much and Jay O'Shea gave them a 2-1 lead just past the hour mark.
Borough were 3-2 ahead within minutes with goals from Rocky Baptiste and Troy Hewitt.
However, two Marcus Bent goals in the final 15 minutes gave Blues a 4-3 win against the Ryman Premier League outfit.
Harrow Borough: Baptiste, Frempong, Watts, Walters, Marney, Leech, Delgado, Ijiha, Green, Morlese, Whitely.
Blues: Butland, Dunphy, Rowe, Kerr, Preston, O'Shea, Valles, Mutch, Newbury, Bent, Asante.