Sexton and Sean O'Brien, who made his first appearance of the season last week against Glasgow Warriors, went off at half-time and Zebre got themselves back in the match with Tito Tebaldi crossing and Daniel Halangahu adding the extras to cut Leinster's lead to 17-7.
However McFadden turned on the style, taking on kicking duties to land a 40-metre penalty before touching down and converting.
McFadden then helped set up Cian Healy to secure the bonus point and grabbed his second score of the night late on, leaving Schmidt with no complaints.
"The match did go to plan, to be honest. We wanted to come away with a good win. The bonus point is exactly that, it's a bonus," said Schmidt.
"We wanted to ensure that we got four points, reintegrated a few guys and, at the same time, not get injuries.
"[O'Brien] was only ever going to play 40 minutes anyway, he and Jonny. It was a decision we had made beforehand.
"It was just a case of Sean needing a bit of game time, Jonny needing to be reintegrated and I thought they both acquitted themselves really well.
"Jonny showed a bit of sharpness. He certainly does like to run although he is more renowned for his kicking and passing game. He does bring, for us, a good running game."
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