Merino made a run into the box and powered home an inviting Matt Ritchie corner to settle a disjointed game littered with fouls and short on chances.
"It is important now to get three points in a difficult game," Benitez told the BBC.
"It is another step forward. We thought that we had to win this game, and (Palace) had confidence and were well organised, so we knew it could be tough.
"The main thing is we keep pushing and winning games."
The result left promoted Newcastle sixth with 14 points from nine games while Palace stayed bottom with three, courtesy of last weekend's shock 2-1 home win over champions Chelsea.
The London club are also the only Premier League side yet to keep a clean sheet this season and lost by the same score as when the two sides last met in the top flight in 2016, when their forward Andros Townsend scored for his former club.
This time round, Townsend was jeered by Newcastle fans in an ill-tempered match and his team mate Yohan Cabaye, another former Newcastle player, was lucky to escape with only a yellow card for a reckless tackle on DeAndre Yeldin.
""We cannot change what the referee decides and move forward," Benitez said of the two-footed challenge before praising Merino.
"We need to put the ball there for him, he went with determination and that was the key."
(Writing by Zoran Milosavljevic,; Editing by Ed Osmond)
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