Musa Barrow and Timothy Castagne's second-half goals on Saturday sent Atalanta two points clear of Inter Milan, who play already-relegated Chievo on Sunday.
But AC Milan responded with Hakan Calhanoglu heading in the only goal against Fiorentina to boost Gennaro Gattuso's team's hopes of a return to elite European football for the first time since 2013-2014.
AC Milan are fifth, one point behind Inter, with Roma a further three points adrift in sixth before they host champions Juventus on Sunday.
"Mathematically, we have only a few points left to go, but it also puts us in a better state of mind going into the Coppa Italia final.
"The team has been extraordinary in terms of mentality." Juventus and Napoli have already qualified for next season's Champions League, but behind them the scramble is frenetic in the chase for the two remaining berths.
Castagne and Duvan Zapata both had goals ruled out for offside in the first 20 minutes of the game at Sassuolo's Mapei Stadium, with Atalanta's home ground undergoing work.
But 20-year-old Gambian Barrow broke through immediately after being substituted on at the break for his first goal this season, with Belgian Castagne adding a second on 53 minutes, finishing off Berat Djimsiti's low cross.
Goran Pandev pulled a goal back for Genoa one minute from time, but the fightback came too late as Atalanta extended their unbeaten run to 11 matches.
- 'On a high' -
Atalanta's next two league games are against Juventus in Turin and back at the Mapei Stadium against Sassuolo on May 26.
"The Champions League is a dream," said Castagne.
"We realised we could fight for fourth place when we completed the comeback against Roma, then beat Juventus in the Coppa Italia.
"Now we'll try to end on a high."
In Florence, French midfielder Tiemoue Bakayoko started for Milan despite his touchline bust-up with Gattuso during last Monday's win over Bologna as the team push for a top-four finish.
Turkish midfielder Calhanoglu headed in Suso's cross on 35 minutes for his second league goal this season, condemning 13th-placed Fiorentina to their fourth consecutive defeat.
"There are six points left, we have to do it," insisted Gattuso, with their final games against relegated Frosinone and midtable SPAL.
"From January until 20 days ago we were in the Champions League, we regret those lost points, but we certainly can't stop believing in it now." Lazio beat Cagliari 2-1 in Sardinia to sit seventh, five points adrift of Inter and the top four.
Napoli play at SPAL on Sunday after Carlo Ancelotti's side secured second place in the league last weekend.
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