Reds boss Benitez sprung a surprise with his team selection at Fratton Park after leaving Kuyt, Xabi Alonso and Fernando Torres on the bench, while also changing to a three-man central defence.
Benitez's substitutions worked perfectly as Kuyt brought the Reds level at 2-2 before Torres headed home a stoppage-time winner.
Dutch attacker Kuyt concedes he would prefer to be starting games, but he understands Benitez's decision to freshen up his team.
"It's the choice of the boss," said Kuyt. "Of course, as a player you always want to play, but it is the manager's choice - and he was right."
SpiritJamie Carragher acknowledged Benitez had taken a gamble and feels the victory at Pompey proves Liverpool's desire to win the Premier League title.
"There are a few times that we've come back, so that tells you about the spirit of the team," said Carragher.
"It's always a gamble when your big names are on the bench.
"But we had extra-time against Everton in the week, so it wasn't about big names but fresh players.
"They came off the bench to make a difference and that's what they did."