The Croatia international struck in the 54th minute to end Liverpool's 12-match unbeaten league run spanning this season and last.
However, the Saints - the last team to defeat the Reds in March - may not have won 1-0 had referee Neil Swarbrick had the benefit of television replays which showed the defender had brought down Daniel Sturridge in the first half.
That incident aside, however, Liverpool did not create nearly enough chances for a team who began the day top of the table.
On this evidence the return of the watching Luis Suarez, sitting out the final match of his 10-match ban, has come not a moment too soon.
Rodgers' sprang a surprise in his line-up by experimenting in defence by selecting four centre-halves - arguably the strongest area of his squad - after naming Kolo Toure on the right and Mamadou Sakho on the left either side of the returning Daniel Agger and Martin Skrtel.
Neither options at full-back looked a success in the first half, failing to supplement their defensive duties with anything approaching the usual attacking roles expected of that position.
Saints' right-back Nathaniel Clyde got forward more than the pair of them in 45 minutes in which his side did not have the majority of possession but were not afraid to commit men to attack.
Sakho, on only his second appearance after a less-than-convincing outing in central defence in the 2-2 draw at Swansea on Monday, is seen as the long-term option in the middle but being broken in at left-back seemed almost like the Reds boss was accommodating the B£16million signing from Paris St Germain for the sake of it.
The watching Jamie Carragher, who patrolled central defence so brilliantly for so many years for Liverpool before his retirement last season, will no doubt have left with plenty of ammunition for his new role as a television analyst.
Sat close to Carragher was Suarez, enduring his last punishment for biting Chelsea's Branislav Ivanovic in April.
He looks set to return for the midweek Capital One Cup tie at Manchester United so this was Iago Aspas' last real chance to impress following his summer move from Celta Vigo.
The Spaniard scored 12 goals last season but has yet to score in five league games for his new club and the fact he lasted only 45 minutes told its own tale.
Liverpool created two real chances in the first half in addition to the penalty shout, a paltry return by anyone's standards.
Goalkeeper Artur Boruc's brilliant one-handed save denied Gerrard's curling free-kick after Aspas had been fouled by Jose Fonte before Sturridge, who after scoring in first four league matches had been unusually quiet, thought he had won a spot-kick.
He cut back on the angle of the penalty area Luke Shaw and Lovren, who made contact with the striker but not the ball.
Victor Moses carved out his own chance when he collected Gerrard's throw down the left, cut in past a couple of defenders only to see Boruc turn his shot behind.
Southampton had probed in the first half without properly testing goalkeeper Simon Mignolet, who created his own problems by coming for a ball Skrtel had covered and could only watch as Adam Lallana volleyed over the open goal.
Chances seemed to be a premium for strikers at both ends as Southampton's England international Rickie Lambert had one sight of goal, from Gerrard's miscontrol, but sliced a gentle looping shot into the arms of Mignolet.
Raheem Sterling's introduction for Aspas at half-time should have injected some life into Liverpool's attack but it was the visitors who struck first in the 54th minute.
Lovren beat Agger to Lallana's corner to head down and past Gerrard on the goalline. It was a goal you sensed had been coming for a while.
The boost in confidence that gave Southampton was evident in Shaw's driving run from halfway which saw Mignolet brilliantly stop both his shot, the rebound off Sakho and then get up to prevent substitute Steven Davis poking home.
Lovren then produced a timely intervention at the other end, diverting Sterling's low cross from the byline destined for Henderson.
In the final 20 minutes Liverpool were back to two regulation centre-backs as Agger and Skrtel were replaced for more attacking options but it did little to change the outcome.
- Sports & Recreation
- Daniel Sturridge
- Mamadou Sakho
- Daniel Agger