The Bees looked dead and buried after Henri Camara's two-goal blast had put Southampton in command.
But two goals in the space of 18 minutes either side of half-time from Rankin and defender Sam Sodje pegged the Premiership side back.
Veteran midfielder John Salako signalled Brentford's intent with a crunching tackle on Camara after only eight seconds.
But the Senegalese international gained his revenge with the opening goal three minutes later.
Graeme Le Saux outpaced Brentford full-back Michael Dobson on the left edge of the penalty area before crossing for Camara to side-foot his third goal in as many matches since a transfer deadline day move from Celtic.
Deon Burton had promised to unveil a shirt of Southampton's arch-rivals Portsmouth if he got his name on the scoresheet.
The former Jamaican international should have done just that in the ninth minute.
Dobson's long throw was only half-cleared by the head of Southampton defender Claus Lundekvam and Burton saw his right-footed volley saved by stand-in goalkeeper Paul Smith.
On-loan defender Calum Davenport then almost doubled Southampton's lead when he headed against the crossbar from a Le Saux corner. Just 12 minutes later Peter Crouch forced a flying save from Brentford keeper Stuart Nelson after flicking Rory Delap's long throw towards the visitors' goal.
Davenport was a thorn in Brentford's side on set-pieces all afternoon and went close again in the 26th minute when he headed narrowly over from another Le Saux corner.
Brentford went close straight from the resulting goal-kick when Jay Tabb volleyed narrowly over.
Captain Stewart Talbot was then denied an equaliser by Le Saux when his 25-yard strike was defected wide by the ex-England defender.
Midfielder Ed Hutchinson headed over from a Tabb corner ten minutes before half-time. Saints were then gifted a second goal by a goalkeeping howler from Nelson.
Nelson, deputising for the cup-tied Ademola Bankole, kicked his clearance straight off the back of Kevin Phillips. The ball rebounded kindly for the alert Crouch who returned the ball to Phillips six yards out.
Nelson made amends for his blunder by saving Phillips' shot but Camara was on hand to tap in his second goal when the ball rebounded into his path.
Brentford's response was swift with former Arsenal striker Rankin getting them back in the match four minutes later.
Rankin received the ball from Sodje midway inside the Southampton half before capping a fine solo run with a right-footed curler which cannoned in off the left-hand post.
Rankin could have drawn Brentford level five minutes into the second half after skipper Talbot had again caused chaos in the Saints' penalty area.
Talbot's shot hit Burton and bounced into the path of Rankin but his scuffed shot was saved by Smith.
Defender Michael Turner produced a superb last-ditch tackle to deny Phillips soon after Camara had played through his strike partner.
Brentford did draw themselves level in the 58th minute when Sodje made it 2-2.
Smith, who was on Brentford's books before joining Southampton last season, completely missed Tabb's right-footed cross, allowing Sodje to head home unmarked at the back post.
MAN OF THE MATCH: Isaiah Rankin (Brentford) – His well-taken goal brought the Bees back into the game just when it looked as though they were dead and buried.