Gian Piero Gasperini's men appeared set to battle it out with Roma for the fourth and final Champions League spot when the division restarted following the coronavirus lockdown, but their excellent form has seen them climb above Inter Milan into third.
They may even be dreaming of an unlikely title challenge after Juve and second-placed Lazio both lost on Tuesday, with Atalanta now just two points behind the capital club.
Inter could retake third when they visit Hellas Verona on Thursday.
Atalanta, who have scored 18 more goals than any other club in the Italian top flight this season, were frustrated for long periods by Sampdoria.
But the home side finally broke through with 15 minutes to play in Bergamo as Brazilian defender Toloi met a corner at the far post to head home.
Colombian international Muriel continued his brilliant first season with Atalanta since signing from Fiorentina, collecting a half-cleared corner before crashing in his 17th league goal of the season in the 85th minute.
It promises to be a thrilling finish to the campaign for Atalanta, with the Champions League 'Final 8' tournament in Lisbon still to come in August.
Roma stayed fifth, albeit 13 points adrift of fourth-placed Inter, as French midfielder Jordan Veretout capped a 2-1 comeback victory over Parma.
Juraj Kucka's early penalty put the away side ahead at the Stadio Olimpico, but Henrikh Mkhitaryan scored for the second game running for Roma before Veretout's 57th-minute winner.
Lozano deepens Genoa woes
Earlier, Hirving Lozano struck as Napoli claimed a 2-1 win over Genoa which left their opponents stuck in the relegation zone.
Genoa, playing their 13th straight season in the Italian top flight, remain one point behind 17th-placed Lecce after their shock 2-1 win over Lazio on Tuesday.
Gennaro Gattuso's Napoli have already qualified for the Europa League after winning the Italian Cup.
Napoli started quickly and midfielder Elif Elmas had a seventh-minute strike ruled out by VAR for a handball by Kostas Manolas in the build-up.
The hosts almost grabbed the lead though when visiting goalkeeper Alex Meret tipped Francesco Cassata's shot against the post.
Napoli instead forged ahead on the stroke of half-time when Lorenzo Insigne fed Dries Mertens, with the club's record goalscorer curling a fine finish from the edge of the area into the bottom corner.
But Genoa hit back to level in the 49th minute as defender Edoardo Goldaniga met Lasse Schone's corner with a firm downward header into the net.
Lozano secured the points for Napoli midway through the second half though, the Mexico winger latching onto a long ball over the top before drilling home his fifth goal of the season left-footed.
Elsewhere, Fiorentina and Cagliari played out a 0-0 draw which leaves both clubs safely positioned in midtable, while Brescia wasted the chance to move within four points of safety as they let a half-time lead slip to lose 3-1 at fellow strugglers Torino.
Sassuolo climbed to eighth in the table after a third consecutive win, beating Bologna 2-1.