The Panthers moved four points clear of the second-placed Warriors, who face Canterbury on Saturday, with an unconvincing victory in which they were forced to play 20 minutes with just 12 men.
Tom Jenkins and Isaiah Papali'i were both sinbinned for professional fouls at CommBank Stadium on Thursday but the Panthers, who didn't take the lead until the 57th minute, were able to prevail.
"That wasn't our best stuff but that was the first time this year when we've had to sort it out and come back," said Panthers coach Ivan Cleary.
"The sinbins ... we had two good periods but the end was super disappointing.
"We got away with a win and there was some good resilience shown which we did last week (in a loss to Brisbane) ... but it's just a game in a season and we'll have to do a lot better than that."
Jenkins scored his 26th try for the year to surpass Rhys Wesser as the most-prolific Panthers player across a single campaign and remains a chance of running down Dave Brown's 38-try season in 1935.
"His all-round game this year has been very consistent and that's why he's getting the tries," Cleary said.
"Rhys Wesser was a try machine and a bit of a legend in our club so it's pretty cool."
Parramatta, meanwhile, will remain in 15th spot and will feel this game was a valuable win they let slip from their grasp.
The Eels had the Panthers on the ropes early when Mitch Moses and Jack Williams put the home side 12-0 up.
Parramatta failed to score across either period while the Panthers were down to 12 men and then let their rivals off the hook in the second half with barge-over tries and pressure-relieving penalties.
"Unfortunately fight and effort only get you so far," said Eels coach Jason Ryles.
"It's a six-again on the last play a couple of times and penalties on play one out of yardage ... they are things that are avoidable and are a little bit around our game awareness that we need to improve."
Jenkins was the catalyst for dragging the ladder-leaders back into the game, catching and offloading a Nathan Cleary kick for Casey McLean to touch down on the left.
Penrith flyer Jenkins was sinbinned on the stroke of halftime for pulling back Brian Kelly as the Eels winger chased after his own grubberkick.
The Panthers trailed 12-6 at the break but Parramatta were unable to use the one-man advantage to their benefit.
And just as Jenkins returned, Liam Henry crashed over under the sticks and Cleary tied the game up with a conversion from right in front.
Liam Martin was next over to push the Panthers six points ahead.
But any hope Parramatta had of getting back into the game was undone by their own ill-discipline as they failed to capitalise when Papali'i was sent to the bin.
Jenkins crossed for his obligatory try afterwards before Williams grabbed a consolation try for the Eels at the death.
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