Inter went ahead after two minutes of the semi-final second leg when Christian Eriksen scored direct from a corner, badly misjudged by goalkeeper David Ospina, but Mertens levelled before halftime with his 122nd goal for the club in all competitions.
Atalanta and Inter in entertaining goalless draw
Napoli went through 2-1 on aggregate thanks to their 1-0 win at San Siro four months ago and will meet Juventus in Wednesday's final in Rome.
Both teams were playing their first game since the end of the three-month stoppage for the coronavirus and the pace dropped considerably in the last 20 minutes despite both teams making the permitted five substitutions.
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