Two moments of class from the German international put the Blues in pole position for all three points but a familiar story of defensive disaster robbed him of a perfect afternoon.
It was all one-way traffic for the hosts in the opening stages as Alex McCarthy was called into action to deny Ben Chilwell and Kai Havertz.
And with the Saints unable to really get to grips on their hosts Werner slotted home a brilliant opening goal.
The former RB Leipzig man dummied Ben Chilwell’s pass to fool Jannik Vestegaard and kept his calm to confidently tuck past McCarthy.
And Werner kept up his one-man battle with Saints defence with an outrageous second goal 12 minutes later.
He did brilliantly to beat the offside trap in behind Jan Bedranek and delicately chipped past the onrushing McCarthy.
But despite barely having a kick in the opening stages, Southampton mustered up a response before the break, as Danny Ings capitalised on Kai Havertz’s error to fire home.
That break in fortune boosted Southampton’s confidence after the break as Chelsea gifted Che Adams an equaliser.
Kurt Zouma’s back pass was a poor one and Kepa could do nothing to prevent Adams from forcing home from close range.
But despite their calamity at the back, Lampard’s side were instantly saved from their horror show as Havertz made amends with powerful finish.
However nothing is ever easy with Chelsea side and with a fourth goal evading them in the final stages they left the door wide open for the Saints.
Zouma was again at fault as he failed to clear his lines in added time and Vestegaard bravely nodded home a late equaliser.
FULL TIME AT STAMFORD BRIDGE IT’S CHELSEA 3 SOUTHATMPTON 3