It was only Preston's second goal at home in the league this season.
Danny Higginbotham was booked after seven minutes for a foul on Chris Sedgwick.
Higginbotham fired over a left-wing cross after 12 minutes and Matt Oakley headed wide of the left-hand post.
Higginbotham again had a 20-yard left-foot free-kick which was caught by Carlo Nash after Chris Lucketti, the Preston captain, fouled Nigel Quashie.
Darren Powell had a right-foot shot deflected by Callum Davidson which wrongfooted the Preston keeper and went high into the top right for an own goal after 27 minutes.
Tomasz Hajto was booked for a foul on Lewis Neal after 37 minutes.
Two minutes were added, but the Saints went in with a one-goal lead at half-time.
Powell narrowly cleared over his own bar three minutes after the re-start when Danny Dichio had mis-kicked in the penalty area.
Chris Sedgwick had a right-foot right-wing cross which was met by a Dichio header, but it went straight at Antti Niemi, the Southampton keeper.
Ricardo Fuller on his return to Deepdale had a right-foot shot inside the left channel from 25 yards saved by Nash.
David Jones, on loan from Manchester United, fired a left-foot shot over the bar and had another shot come cross which went over the bar.
Agyemang equalised for Preston with a great foot turn and shot into the top left-hand corner of the net from 18 yards after a Neal left- wing cross had been dummied by Dichio.
Jones made a great run through the Southampton defence and shot wide of the right-hand post late on, but 1-1 was a fair result.