First-half goals from Mauro Icardi and Ivan Perisic - either side of a Manuel Pucciarelli equaliser - was enough for Inter to secure the points, and a fourth-placed finish, in their last match at San Siro this season.
Inter were top of the table by the mid-season break, but a disappointing second half of the campaign saw their title hopes fade and they also fell away from contention for the Champions League.
Head coach Mancini is adamant Inter have made clear progress this term, but accepts there is plenty of work to do to return Inter to the top domestically and in Europe.
"We would not have finished fourth if we did everything right. The position is what we deserve, because we threw away what we had done for the first six months," Mancini told Tuttomercatoweb.
"In Italy we are quick to criticise all aspects of a team, but instead you have to see the good things that a team does, and we have made progress.
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"We will seek to strengthen the team, but this is still the best season of the last five years.
"We thank the fans who came to San Siro, we hope next year to be able to give them some extra satisfaction."
Mancini believes the victory at Empoli shows the manner in which Inter must close out matches if they are to reduce the gulf in class between themselves and champions Juventus.
"We have to improve many things, the technical quality, the desire to fight and we must learn not to give anything away in times of difficulty, like how Juve do," he added.
"Surely we have to improve our quality, this is crucial. The gap between Juve and the other teams is huge."