The Italian's first title of the year was his ninth overall but first at Masters level.
Lajovic's run to his first career final was unexpected. But the unseeded Serb rarely threatened in humid, overcast and slightly windy conditions.
Fognini needed a medical timeout to receive treatment to his right foot and right thigh after the fifth game of the second set.
But it did not impede him as he served out the match, clinching victory on his second match point when Lajovic hit forehand wide.