Boston boss Steve Evans informed referee Phil Prosser of tthe incident at half-time, and it will be included in his match report.
It is alleged that around 10 home fans made monkey taunts towards Abbey.
Rochdale chairman David Kilpatrick said: "Rochdale is a community with a high thnic population - we have never had any orchestrated racial abuse at the club and I wouldn't condone it."
Boston also wrote to the FA complaining of racist chanting towards Abbey and team-mate Danny Thomas in last week's game with Mansfield Town.
Speaking after that game at Field Mill, Abbey said: "I knew I would get stick because I played for their rivals Chesterfield, but all of a sudden there was a group who started monkey chants.
"Danny told me he heard monkey chants in the first-half when he took corners.
"We spoke and decided to make an official complaint, we shouldn't have to tolerate it."