Leading by 32 points early in the last quarter, the Magpies had to withstand a late onslaught from their bitter rivals in a Saturday night classic in front of 86,879 fans at the MCG.
Carlton booted the final five goals, but it wasn't enough as the Magpies saluted 12.12 (84) to 11.15 (81) to keep their premiership defence alive.
McGovern had the chance to give the Blues one of their greatest-ever victories when he pushed forward to mark the ball about 45m from goal.
But while he kicked a similar goal for Adelaide to draw a game against Collingwood at the same venue in 2017, this time he sprayed the ball out on the full.
"When the siren went I just put my hands in the air, it's like what do we do we have no control over what's about to happen," Pendlebury said.
"I feel like we played really well for three quarters.
"We probably went a little bit safe back into our shell in that last quarter, but for three quarters it felt really like a Collingwood game of footy."
Fielding their strongest team for months, the Magpies recaptured close to their best form to pay tribute to Pendlebury becoming the sixth VFL/AFL player to reach 400 games.
Pendlebury, who during the week announced he would continue next year for a 20th season, was brilliant in his milestone match, gathering 27 possessions and nine clearances.
The former long-term captain came close to a highlight for the ages, hitting the post after snapping a shot from the pocket in the first quarter.
Carlton kicked the final five goals of the game but still came up short against Collingwood. (Morgan Hancock/AAP PHOTOS)
Carlton captain Patrick Cripps put in an epic final quarter, almost lifting the Blues to victory by himself as he continually charged out of the centre clearances.
If Collingwood are to book a finals berth they will likely need to do it without star playmaker Jordan De Goey, who hobbled off late in the third quarter with what coach Craig McRae described as a "high-grade" hamstring injury.
De Goey has been managing a groin issue for months and sat out last Sunday's win against Richmond.
But the premiership star looked back to his supreme best, booting two goals in a lively performance before he limped off the field for likely the last time this season.
Carlton midfielder Adam Cerra suffered his third hamstring injury of the campaign when he was subbed out in the second quarter, replaced by Matt Kennedy.
The Blues were forced to play with just three on the bench in the final term after Matthew Cottrell hurt his shoulder.
After sitting second a fortnight ago, Carlton's fourth defeat from their last five matches leaves them clinging to a finals spot. They could finish the round as low as eighth.
"Really pleased that our group decided not to give up ... we went to line," Blues coach Michael Voss said.
"Really disappointed in one part, but enormously proud that we were able to fight that game out right to the end when we could have chosen something else."
With three games to go, Collingwood sit 10th and only a game outside the top eight.
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