Higuain took his league tally to 32 goals with a double in Napoli's 2-1 home win over Atalanta and Totti cracked in a spectacular free kick which helped Roma to a 3-2 win at Genoa.
The results left Napoli in second position on 76 points from 36 games, two more than Roma with two games remaining.
Juventus secured their fifth successive Italian title last month, leaving their rivals to battle it out for the other automatic group stage berth in Europe's premier club competition.
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The top two qualify automatically for the money-spinning group stage while the third-placed team enter a playoff round.
The evening began with 39-year old Totti rolling back the years as he came on in the second half with Roma trailing 2-1 after Mohamed Salah had given them an early lead.
Having had their advantage wiped out by the club's former midfielder Panagiotis Tachtsidis and Leonardo Pavoletti, Roma forced the final twist thanks to a moment of magic from their inspirational stalwart.
Totti scored his fourth goal in as many games as a substitute when he unleashed a ferocious shot from 25 metres which spun away into the top left corner.
He also forced a superb save from Eugenio Lamanna with another free kick but the keeper could do nothing about Stephan El Shaarawy's simple finish in the 87th minute after Edin Dzeko squared the ball to the striker.
Needing a win to reclaim second place, Napoli made heavy weather of their victory over 13th-placed Atalanta.
Higuain fired them into a 14th-minute lead and doubled the advantage with a superb header in the 77th.
The home side missed a hatful of chances as Atalanta keeper Marco Sportiello pulled of a string of good saves before a Raul Albiol own goal set up a tense finish.
(Writing by Zoran Milosavljevic; Editing by Ken Ferris and Ed Osmond)
