Antonio Conte's men enjoyed the majority of possession in the opening period, and seconds into the second half they took the lead thanks to wonderful composure from Olivier Giroud.
The Frenchman, who is vying for Chelsea's centre-forward spot with Alvaro Morata, has now scored four times since joining from Arsenal in January, but the Spaniard also had his say at Wembley.
Less than two minutes after coming on for Giroud, Morata produced a powerful downward header past Alex McCarthy from Cesar Azpilicueta's cross to seal the win late on.
Even Chelsea fans accept that Morata has really struggled at times this season, and with that in mind, they really appreciated what the striker did straight after scoring against Southampton.
What Morata did straight after scoring v So'ton
Morata's 82nd-minute header at Wembley was his 15th goal of the 2017-18 campaign from 44 appearances so far, and right after hitting the back of the net, he produced a lovely gesture.
As you can see below, after checking to ensure he wasn't offside, Morata ran towards to jubilant Chelsea fans and immediately put his hands together in an attempt to ask for forgiveness.
Chelsea fans react on Twitter
Blues supporters who spotted his celebration, which also included a tapping of the badge, feel he was apologising to them for his frustrating debut season at the club.
As you can imagine, Chelsea fans loved Morata's gesture and praised what they feel is a sign of strong mentality - check out the best tweets below.
Morata's 2017-18 campaign
In a summer which saw transfers like Romelu Lukaku to Man Utd and Alexandre Lacazette to Arsenal, Chelsea signed Morata from Real Madrid for a club-record fee of around £60 million.
The 25-year-old bagged 20 goals under Zinedine Zidane last season but has missed several big chances this term, leading people to criticise his inability to be clinical in front of goal.
One thing that hasn't been questioned, however, is Morata's heading ability, and he'll be hoping to play a major part in the final few weeks of the season, which ends with the FA Cup final.
What do YOU make of Morata's gesture to Chelsea fans after his goal against Southampton? Do YOU think he has what it takes to improve next season? Have YOUR say in the comments box below!