That loss was the heaviest of Diego Simeone's seven-year spell at Atletico, but his side have now taken 14 points from a possible 18 to climb to the summit.
Antoine Griezmann's improvised volley flew over the crossbar as Atletico made a slow start in response to their Champions League humiliation.
Ruben Pardo fired off target twice in quick succession but Atleti took the lead shortly before half-time.
Angel Correa did brilliantly to turn away from Kevin Rodrigues and Raul Navas could only deflect the low cross out for captain Godin to finish smartly into the bottom-right corner.
And it was another defender who struck the decisive second goal on the hour-mark.
Filipe Luis, a half-time replacement for World Cup-winning defender Lucas Hernandez who went off as a precaution with a muscle problem, sent a smashing finish into the top-right corner, giving former Atletico goalkeeper Miguel Angel Moya no chance.
Diego Costa fired straight at Moya as Atletico sought to extend their lead, but Simeone and his side can watch El Clasico from their lofty position atop LaLiga.
What does it mean? Atletico find a way
It was a mostly stodgy performance from Atletico, who took time to find their stride in the first half. But, as they so often do under Simeone, they found a way to win the game despite failing to produce their best football. They head to Leganes next weekend and will expect to collect another three points against the strugglers. The title race is very much on.
Godin leads from the front
Uruguay centre-back Godin is far from a regular goalscorer - he last found the net in LaLiga back in March 2017 - but he stepped up when his team needed him with an unerring strike of which a striker would have been proud. Filipe Luis' goal was a cracker too and he has now scored in consecutive league appearances.
Pardo misses cost visitors
Sociedad were seeking a third straight LaLiga away win and they arguably deserved to be in front at half-time. But Pardo missed their clearest two sights of goal and Godin punished those misses. Once ahead, Atletico were unlikely to give up their lead and they have now kept a clean sheet in 18 of their last 26 home league matches.
Key Opta Facts
15 - Rodrigo Hernandez made 15 recoveries against Real Sociedad, more than any other Atletico de Madrid player in a game this season in all comps. Oxygen. pic.twitter.com/bayuDZabhH— OptaJose (@OptaJose) October 27, 2018
- Atletico are the only team from the top five European leagues yet to concede a goal in the first half of games this season.
- Godin scored his first non-headed goal in LaLiga since September 2012 against Real Valladolid. His previous 11 league goals were headers.
- Atletico have not conceded a goal in LaLiga this season while Rodrigo has been on the pitch (529 minutes played).
- Costa has failed to score in his last 17 league games, his longest drought between LaLiga and the Premier League.