The referee halted the game after three minutes when Eto'o was subjected to some racist taunts from the home fans.
The match resumed after a public announcement was made asking the fans to stop the chants.
Cameroon's in-form striker Eto'o played on his own upfront due to the absence of Argentinean Diego Milito.
He scored the match's only goal in the 39th minute in superb fashion to take his tally to six goals in seven games.
Eto'o evaded his challenger on the edge of the area before planting a left-foot shot into the corner of the net.
The 29-year-old, who joined Inter from Cagliari in the summer of 2009, celebrated his goal by dancing like a monkey.
"We are not dependent on Eto'o. When I have a more complete squad to choose from, we will have more alternatives and styles of play," Inter coach Rafael Benitez said.
The victory sent title holders Inter level on 14 points with arch-rivals AC Milan at the top.