Kvitova's victory in the first reverse singles gave the Czechs an insurmountable 3-0 lead in the first-round match and secured a 10th straight appearance in the last four. They will face Germany or Belarus in the April semifinals.
The second reverse singles was not played but Switzerland's Timea Bacsinszky and Jil Teichmann defeated Lucie Safarova and Barbora Strycova 1-6, 6-4, 10-8 in the doubles to make the final score 3-1 to the Czechs.
The 27-year-old Kvitova, who triumphed at Wimbledon in 2011 and 2014, secured the win against Bencic on her first match point.
"It was better today than yesterday, when I played in the Fed Cup again after such a long time away and needed time to get used to it," she said. "It was a good game from both of us but I wasn't so nervous as yesterday."
The big-hitting Czech player put her opponent under pressure with aggressive strokes on the indoor hard court at Prague's O2 Arena, breaking serve twice in the opening set.
Kvitova, who hit a total of 10 aces, then got the decisive break for a 4-3 lead in the second set after Bencic sent a forehand long.
It was a memorable return to the Fed Cup for Kvitova after she was injured in a knife attack at her home in December 2016.
Kvitova, who won the St. Petersburg Open in Russia earlier this month, was a member of the Czech team that won five of the last seven Fed Cups.
Karolina Pliskova, the Czech No. 1, missed the first-round match against the Swiss because of illness.