Gregory Vignal's controversial late penalty saw Southampton deny rock-bottom Scunthorpe victory.
The Iron had Matt Sparrow sent off for foul play but were handed a penalty when Ian Pearce fouled Martin Paterson.
Kelvin Davis saved Andy Crosby's kick but Crosby buried the rebound to give Scunthorpe the lead.
But Saints levelled when the referee awarded a penalty for an off-the-ball incident involving Bradley Wright-Phillips and Vignal hit home.
Scunthorpe manager Nigel Adkins on referee Jonathan Moss's decisions:
"Our objective was to get three points and we should have, but two refereeing decisions have cost us.
"They're both wrong decisions, I've looked at the videos and am quite happy to talk about it.
"There are things like that we can't control. The officials have cost this club dearly."
Nigel Pearson on his first point as Southampton boss after a week at the helm:
"To sum up my first week it's certainly been tough. This is one point and I'm not getting carried away.
"We came here to be slightly more organised than we were against Plymouth in midweek and I think from that we've got a foundation to build on.
"I was pleased with how the players tried to put into practice what we've been working on."
Scunthorpe: Murphy, Hobbs (Iriekpen 46), Crosby, Butler, Williams, Cork, Goodwin, Sparrow, Morris, Paterson (May 89), Horsfield (Forte 67).Subs Not Used: Lillis, Hayes.
Sent Off: Sparrow (54).
Booked: Butler, Williams.
Goals: Crosby 41.
Southampton: Davis, Thomas (Wright-Phillips 70), Pearce, Davies, Vignal, Viafara (Licka 79), Idiakez, Wright, Surman (Hammill 57), Saganowski, John. Subs Not Used: Poke, Euell.
Booked: Vignal, Hammill.
Goals: Vignal 88 pen.
Ref: Jon Moss (W Yorkshire).