Benitez's side trailed 2-0 at half-time to goals from Dominic Calvert-Lewin and Richarlison, who scored either side of Matt Ritchie having a penalty saved by Jordan Pickford at St James' Park on Saturday.
But Perez set up Rondon to get Newcastle back in the game after the interval, with the former then scoring twice in three minutes to lift the Magpies up to 13th.
Benitez was effusive in his praise for Perez and Rondon after Newcastle's fifth consecutive Premier League home win.
"This team is important," Benitez told Sky Sports. "The link between Ayoze Perez and Salomon Rondon, if Messi was doing that everybody would be talking about the goal."
Newcastle last came from two goals down to win a Premier League game in October 2003, with Benitez explaining the tactical tweak that helped his side's comeback.
"Normally I say to the players stay calm at half-time, score one goal and get back into the game," Benitez said. "In the first half we had chances to score but they scored two goals.
"We changed the shape of the team - with Ritchie on the right and four at the back. We were winning more second balls in the second half."
3-2 - Newcastle United came from two goals down to win a Premier League game for the first time since October 2003 against Fulham under Sir Bobby Robson. Thriller.— OptaJoe (@OptaJoe) March 9, 2019
Everton have taken only four points from their past six Premier League games but Marco Silva felt decisions by referee Lee Mason and his assistants contributed to the Toffees surrendering their lead.
"Of course this is difficult," Silva said to Sky Sports. "We led 2-0 then we had four counter-attacks to kill the game. We kept giving belief to our opponent.
"I told the team even at half-time we had to keep doing what we did in the first half. We lost some counter-attacks after the break. After we conceded we gave some belief to them.
"When they made it 2-2, the game changed completely. The third goal was offside. Rondon was in an offside position. It's really strange to talk about the situation."
Asked why he approached referee Mason at full-time, Silva added: "They gave one penalty to them but not us when Gylfi Sigurdsson [was fouled]. Then the third goal was a clear offside. Rondon was in a clear offside position."