Rooney played the full game as Manchester United eased into the fourth round thanks to a 3-1 victory against the League One side but he failed to trouble the scoresheet.
"It was a massive challenge but I thought Zander (Diamond) and I coped quite comfortably with Rooney for the majority of the game," Zakuani told the Northampton Chronicle.
"We didn't really get split open as a back four which is positive and it can only stand us in good stead for the League One campaign when you play against those players and they don't create many chances.
"We thought we frustrated them, we kept our shape and we were hard to break down.
"We feel disappointed with the goals we conceded because we made it easy for them.
"But I thought we played really well as a team. We were solid and hard to break down."