Grzegorz Rasiak opened the scoring when he capitalised on Romain Larrieu's error to coolly slot in.
He made amends with a leveller into the top corner from 12 yards before being dismissed and Argyle's David Norris had a late effort ruled out for offside.
Southampton boss George Burley
"There were a lot of tired legs out there. That's our second game in three days on rain-sodden pitches.
"We are pleased to get a point because we never got our game going at all.
"But under the circumstances I think it is hard to be critical when you have put so much in with the two games in three days. It's not easy."
Plymouth: Larrieu, Gosling, Doumbe (Summerfield 35), Seip, Sawyer, Norris, Buzsaky (Dickson 80), Nalis, Capaldi, Samba (Reid 55), Hayles.
Subs Not Used: McCormick, Aljofree.
Sent Off: Hayles (84).
Booked: Norris, Hayles, Buzsaky.
Goals: Hayles 66.
Southampton: Davis, Ostlund, Lundekvam, Baird, Bale, Prutton (Makin 46), Wright, Pele, Skacel (Licka 46), Wright-Phillips (McGoldrick 80), Rasiak.
Subs Not Used: Bialkowski, Sarmiento.
Booked: Bale, Davis, Pele.
Goals: Rasiak 5.
Ref: K Wright (Cambridgeshire).