Three consecutive defeats raised some concerns for the Panthers but Cleary steadied the ship with his magic touch at a packed WIN Stadium on Saturday.
The superstar halfback threw the last pass for two tries and had one of his own, ensuring the four-time premiership winners would hit finals with a spring in their step.
"A lot of it today was good," coach Ivan Cleary said.
"There's a few things we can definitely learn from, which we will. We're just ready to start the new comp, grateful to be there."
The result locks up a seventh-placed finish and a trip to Auckland to face the Warriors, captained by one of the chief architects of Penrith's premiership dynasty in Fisher-Harris.
"He's an absolute beast. Everyone knows that," said Nathan Cleary.
"I've played a lot of footy with him and now to verse him in a finals game over there, it's another exciting story to add to what we're going to do."
The order of the top eight is now set, with fifth-placed Cronulla to host the Sydney Roosters in next weekend's other elimination final.
The Panthers looked on track for victory stretching to a 22-6 lead with two four-pointers in the eight minutes before halftime.
Tom Jenkins kicked inside off his left foot to help Casey McLean over the line before Cleary put Luke Garner into a hole and ran in support for the Panthers' fourth try.
Cleary had earlier sent Paul Alamoti over with a bullet-like cut-out pass on the right edge.
Clint Gutherson finished a strong first year at the Dragons by sending Corey Allan and Tyrell Sloan over to close the gap to eight points in the second half.
But Gutherson gifted Penrith a golden opportunity to move closer to victory when he was penalised for dissent as the last 15 minutes approached.
At point-blank range, Cleary's flat pass put Lindsay Smith over for the try that confirmed the Panthers' win.
Replacing the rested Brian To'o, Alamoti confirmed his double on a shift down the right side in the final 90 seconds.
The loss brings the curtain down on Shane Flanagan's second season coaching the Dragons, who lost Christian Tuipulotu to a hamstring issue in the warm-up.
It was the final blow in a rough season of injuries for the Red V, set to finish in 15th place despite some gritty showings earlier in the season.
"I've learned a lot this year about some individuals and the team," Flanagan said.
"In the end, because of the injury toll that we've had, the lack of that class in real crucial moments has probably hurt us a bit.
"We just can't get it done when we need to."
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