Eusebio Di Francesco's side were dominant for much of Saturday's clash at Stadio Olimpico, with Lazio unable to replicate the form that has seen them win nine consecutive games in all competitions.
After Edin Dzeko had gone close on three occasions prior to the interval, Roma finally got a deserved breakthrough four minutes after the restart - Perotti keeping his cool from 12 yards following Bastos' foul on former Lazio defender Aleksandar Kolarov in the box.
Roma doubled their tally four minutes later when Nainggolan drove forward with purpose before planting an unerringly accurate finish into the bottom-left corner, giving Thomas Strakosha no chance.
Lazio were given a lifeline with 20 minutes remaining, however, as - after utilising the video review system - the referee awarded a penalty for Kostas Manolas' handball.
Ciro Immobile stepped up to thump home and set up a grandstand finish, but Roma held firm despite late pressure from the visitors, with Marco Parolo going closest for Lazio.
The victory lifts the Giallorossi above their city rivals and Inter into third place, as Serie A's title race intensifies.
