The Brazilian midfielder opened the scoring after 29 minutes with a superb left-footed shot from the edge of the area.
Forward Mario Balotelli, back in the squad after apologizing to Inter coach Jose Mourinho for an unidentified row, doubled their lead seven minutes after the restart.
He side-footed a deft pass from Argentinean striker Diego Militi past the keeper at the near post.
Motta put the icing on the cake five minutes from time with a low shot after a neat exchange of passes with Dejan Stankovic.
Inter, who were missing Samuel Eto'o, Maicon, Lucio and captain Javier Zanetti due to suspension, are still on top of the league table with 66 points.
They are one point ahead of second-placed Roma, who kept pace with a 1-0 victory at Bari.
Montenegrin striker Mirko Vucinic scored the winner after 19 minutes.
Inter 3-0 Bologna