Substitute Zaniolo decided a hard-fought encounter in Sardinia by stroking home Raoul Bellanova's cut-back in the 66th minute and moving Atalanta five points clear.
Fiorentina earlier remained on Napoli's heels after their 1-0 home win over Cagliari in their first league match since midfielder Edoardo Bove's sudden collapse last weekend.
Spaniard Raya dived low to his right to beat out Mateo Retegui's spot kick in the 51st minute then sprang across his goal to claw away the forward's follow up header.
Inter Milan thrashed Atalanta 4-0 on Friday to move provisionally top of Serie A, while Torino snatched a late 1-0 win at Venezia to continue their positive start to the campaign.
Gian Piero Gasperini lavished praise on his "incredible" Atalanta players after they stunned Bayer Leverkusen to win the Europa League and claim their first ever continental honour.
Ademola Lookman scored a stunning hattrick as Atalanta ended Bayer Leverkusen's 51-match unbeaten run to win the Europa League final 3-0 on Wednesday and claim their first trophy for 61 years.
Bayer Leverkusen had won only two major trophies in their 119-year history before this season but on Wednesday the newly-crowned Bundesliga champions have the chance to claim a double when they face Atalanta in the Europa League final in Dublin.
Dusan Vlahovic shot Juventus to the Italian Cup with the only goal in Wednesday's final against Atalanta who were denied a first trophy in six decades.
Bayer Leverkusen stretched their season-long unbeaten run to 50 games with a 5-0 win at 10-man Bochum on Sunday.
Substitute Zaniolo decided a hard-fought encounter in Sardinia by stroking home Raoul Bellanova's cut-back in the 66th minute and moving Atalanta five points clear.
Fiorentina earlier remained on Napoli's heels after their 1-0 home win over Cagliari in their first league match since midfielder Edoardo Bove's sudden collapse last weekend.
Spaniard Raya dived low to his right to beat out Mateo Retegui's spot kick in the 51st minute then sprang across his goal to claw away the forward's follow up header.
Inter Milan thrashed Atalanta 4-0 on Friday to move provisionally top of Serie A, while Torino snatched a late 1-0 win at Venezia to continue their positive start to the campaign.
Gian Piero Gasperini lavished praise on his "incredible" Atalanta players after they stunned Bayer Leverkusen to win the Europa League and claim their first ever continental honour.
Ademola Lookman scored a stunning hattrick as Atalanta ended Bayer Leverkusen's 51-match unbeaten run to win the Europa League final 3-0 on Wednesday and claim their first trophy for 61 years.
Bayer Leverkusen had won only two major trophies in their 119-year history before this season but on Wednesday the newly-crowned Bundesliga champions have the chance to claim a double when they face Atalanta in the Europa League final in Dublin.
Dusan Vlahovic shot Juventus to the Italian Cup with the only goal in Wednesday's final against Atalanta who were denied a first trophy in six decades.
Bayer Leverkusen stretched their season-long unbeaten run to 50 games with a 5-0 win at 10-man Bochum on Sunday.
Atalanta's passage to the Dublin final, where they will face Bayer Leverkusen, later this month was fully deserved after a dominant performance in which Marseille barely had a kick in yet another poor away display from the Ligue 1 outfit.
