Howard rammed home his 13th league goal of the season to give Derby their sixth successive Championship win.
Derby weathered a first-half storm, as first Rudi Skacel and then Jhon Viafara struck the woodwork for Saints.
The Rams improved after the break and Howard's goal inflicted Saints first home defeat since September.
Derby boss Billy Davies:
"There's a long way to go and I'm not letting the players get carried away with how well we've done so far.
"We're on a good run at the moment but this is a hard division to get out of.
"Southampton were the better team in the first half and at times were tearing us apart before I made a change to get us competing in midfield."
Southampton: Davis, Baird, Lundekvam, Pele, Bale, Wright, Idiakez, Viafara, Skacel (McGoldrick 54), Rasiak (Dyer 77), Saganowski (Wright-Phillips 53).
Subs Not Used: Bialkowski, Ostlund.
Booked: Idiakez, Baird.
Derby: Bywater, Edworthy, Leacock, Moore, Camara, Oakley (Mears 86), Jones, Malcolm (Teale 35), Fagan (Barnes 53), Pearson, Howard.
Subs Not Used: Michael Johnson, Lupoli.
Booked: Howard, Fagan, Barnes.
Goals: Howard 83.
Referee: J Moss (West Yorkshire).