In the second minute of injury time, the 31-year-old intercepted a pass just outside the box, beating four men before chipping his final effort beyond goalkeeper Sean Johnson as crew run out 4-1 victors in the first leg encounter.
"Harrison has been good," Berhalter said, as reported by his club's official website.
"The focus that he had before the [Atlanta United FC] game was tremendous.
"In training, the intensity and the movement, and there was no surprise that he had a good game against [Atlanta United FC].
"To follow it up [against New York City] was important for him. He needs to establish that he can continue to play at this level.
"We know that he is high-level fullback for this league, and he just needs to keep doing it because he is quality."
The goal was Afful's first of the MLS season, having played 26 games - 23 of which he started.
He is in his third season at Crew after joining in June 2015 from Tunisian giants Esperance.
The second leg of the conference clash is set for the Yankee Stadium, New York, on Sunday.