A frustrated Higuain was thwarted by goalkeeper Denys Boyko as the Serie A side pressed for a second goal.
Seleznyov then took advantage of slack Napoli defending to snatch an equaliser with nine minutes left to put the Ukrainians in pole position for a place in the final in Warsaw.
Holders Sevilla beat Fiorentina 3-0 in their first leg in Spain to take charge of the tie ahead of next week's return.
Napoli coach Rafael Benitez suggested Dnipro's goal was offside, telling reporters: "Everyone saw what happened with the goal that changed the game. But we have to bear in mind our excellent performance in the second half when we created a lot."
Napoli, whose only European triumph was lifting the UEFA Cup in 1989, struggled to break down a stubborn Dnipro defence in the first half in Naples and, on the only occasion they got through, Lorenzo Insigne's shot struck the post.
The hosts appeared to have done the hard part when Spaniard Lopez headed them in front five minutes after halftime.
A second goal looked imminent as gaps began to appear in the Dnipro defence, but Dnipro keeper Boyko had other ideas.
Higuain twice got clear on the right but Boyko saved both efforts with his legs, and did the same when the Argentine got free on the left for another chance.
The Dnipro stopper then tipped a rising shot over the bar after Higuain worked an opening on the edge of the area.
Dnipro, playing their 17th match of a campaign which began in the third qualifying round on July 30, hit back against the run of play with nine minutes left.
Artem Fedetskiy sent in a low cross from the right, the Napoli defence failed to clear and Seleznyov turned it in at the back post to completely change the complexion of the tie.
(Writing by Brian Homewood; Editing by Ken Ferris)
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