Mirko Vucinic's and Marco Cassetti's first-half goals put Roma on 68 points, one more than Inter, who drew 2-2 at Fiorentina on Saturday as their domestic form falters under the stress of reaching the Champions League semi-finals.
Third-placed AC Milan's title hopes diminished after they slipped four points off the pace with five games to go despite coming from 2-0 down to draw 2-2 at home with Catania thanks to Marco Borriello's double.
The title race is far from settled but the leadership change still marks a remarkable reversal.
Inter had been in sole command since October and looked to be cruising to a fifth straight scudetto in mid-February when they led by nine points.
By contrast, Roma have rallied after they were in seeming disarray early in the season when Claudio Ranieri replaced Luciano Spalletti.
Montenegro forward Vucinic put them ahead on 12 minutes with the help of a blunder by Atalanta keeper Andrea Consigli, who allowed a powerful but direct shot to slip through his grip.
Cassetti headed in a Francesco Totti cross in the 27th minute as Roma extended their unbeaten league run to 23 matches.
Simone Tiribocchi capitalised on some poor defending to pull one back in the 53rd for third-bottom Atalanta, four points behind Bologna, who blew a two-goal lead in a 3-2 home defeat to fellow strugglers Lazio.
STRONG COMEBACK
Catania's Argentine forward Maxi Lopez stunned the San Siro by running on to Adrian Ricchiuti's threaded pass and steering the ball into the far corner in the 12th minute.
Lopez returned the favour with a cross for Ricchiuti to head home and make it 2-0 for the visitors in the 43rd before Milan came back strongly in the second half.
Forward Borriello headed in soon after the break and fired the equaliser 10 minutes from time but the hosts were unable to snatch a winner despite intense pressure in the closing stages.
Palermo and Sampdoria remain neck-and-neck in the contest for Italy's fourth and final Champions League place with 54 points a piece after victories over Chievo Verona and Genoa respectively.
Fabrizio Miccoli struck twice to help Palermo beat Chievo 3-1 at home.
Antonio Cassano's header in the 23rd minute gave Samp a 1-0 win in a city derby that started 15 minutes late because the team coaches were caught in traffic and was marred by fans clashing with police outside the stadium.
Troubled Juventus are three points behind in sixth after a 1-0 home win over Cagliari with Italy defender Giorgio Chiellini nodding home in the 35th.
Bottom side Livorno lost 2-0 at home to Udinese, with Gennaro Ruotolo's return to the dugout after Serse Cosmi was sacked failing to raise their forlorn hopes of survival.
Siena, one
