The winger, who has featured for Roma just three times, spent last season on loan at Cesena, helping the club to promotion from Serie B.
D'Alessandro will now get a chance to test himself on a regular basis in Italy's top flight after moving to Atalanta.
Roma, who were runners-up to champions Juventus last season, also revealed on Friday that Marquinho has agreed a €1 million season-long loan move to Al Ittihad.
The Brazilian has made 56 appearances for Roma, whom he represented on loan before signing a permanent deal in 2012.
However, he was shipped out to Verona last season and will now head to Saudi Arabia.
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