But despite surrendering the lead, Bombers coach James Hird could not have been more proud of his players as they took the field under immense pressure while the club is under investigation for its supplement use last year.
Hird heaps praise on players and club
"I've been so proud of the players at the Essendon Football Club for the last 10 days," Hird said post-match.
"They have just shown a strength of character not many people have, and they have been resilient, they have been focused on their footy when, I can imagine, they would have just liked to be focused on themselves.
"Tonight's performance, with everything that was going on in the background, was terrific"
Essendon fans keep the faith
And if not for a slight bit of panic late in the game, the Bombers would have finished the night unbeaten after earlier accounting for the Western Bulldogs.
The Magpies appeared out of the game when they trailed by 11 points with only two minutes remaining, before forward Andrew Krakouer kicked a goal that closed the gap to five points.
Pies' class rises to sink spirited Dogs
A near miss to speedy small man Jamie Elliott followed, before Travis Cloke was awarded a contentious free kick 15 metres from goal and kicked truly.
With only 13 seconds left at the final bounce, Essendon youngster Luke Davis won a free kick 55 metres from goal before the siren sounded. His drop-punt attempt at goal fell two metres short, giving the Magpies the 1.2.10 (31) to 0.4.5 (29) win.
Reigning Copeland Trophy winner Dayne Beams was important for the winners with 12 disposals but he was one of few major contributors for the Magpies.
Ben Johnson, who sat out of Collingwood's earlier win over the Western Bulldogs, showed some run with nine touches and three inside-50 entries.
And Brent Macaffer, in his first appearances since rupturing his anterior cruciate ligament in February last year, also showed some zip.
Coach Nathan Buckley praised Macaffer for his turnaround in professionalism.
"Day in day out, his application to his footy is chalk and cheese to what it was 18 months ago," Buckley said.
"He's quite obviously got some talent, and he's adding the professionalism and dedication to it and we're hoping that's a good mix."
For the Bombers, there were encouraging signs that their attempts to make in-roads in 2013 will not just be based on the recruitment of Brendon Goddard.
Although Goddard was important with 10 disposals and a goal, it was a number of lesser lights who were also important.
Davis got his first taste of the big time with one of footy's toughest jobs - running with and attempting to stop Collingwood champion Scott Pendlebury (10 disposals).
Dyson Heppell took on more responsibility with a number of his more senior midfield teammates missing, and Tom Bellchambers went a fair way to stamping himself as Essendon's first-choice ruckman with a strong display around the ground and near goal.
However, this was only the opening night of the NAB Cup and these sides were poor versions of themselves compared to what they will be come round one.
The Bombers were missing captain Jobe Watson, and fellow midfielders Jake Melksham, David Zaharakis, Ben Howlett and Jason Winderlich.
The Magpies were without Luke Ball, Alan Didak, Alex Fasolo and Dale Thomas, but also rested Dane Swan and Heath Shaw for the clash after the pair had impressed against the Bulldogs earlier in the night.
WHAT THE COACHES SAID
Collingwood coach Nathan Buckley: "I think it's one of those ones where the team in front just tries to chew up the clock a little bit. We were in scoring range for the best part of the last three or four minutes and we were able to kick a few goals and we were very fortunate in the end."
Essendon coach James Hird: "It's always great to play footy. We'd rather be playing footy without this hanging over our head, that would be more of a relief, but that's not going to happen for a while. We just really enjoyed tonight [and it was] just really good to see the Essendon players out there playing football after six months off."
Fantasy snapshot
It was a positive return for Brent Macaffer (FWD, $132,600), who gathered six disposals plus three tackles to find 30 points. At his price, Macaffer offers some real value and if he can stay fit and in Collingwood's best team, Fantasy coaches will have a close eye on his progress.
COLLINGWOOD 1.0.5 1.2.10 (31)
ESSENDON 0.2.3 0.4.5 (29)
SUPERGOALS
Collingwood: Sinclair
Essendon: Nil
GOALS
Collingwood: Krakouer, Cloke,
Essendon: Jetta 2, Heppell, Goddard
BEST
Collingwood: Beams, Pendlebury, Russell, Sinclair, Johnson
Essendon: Dempsey, Baguley, Stanton, Goddard, Pears, Heppell
INJURIES
Collingwood: Nil
Essendon: Nil
Reports: Nil
Umpires: TBC
Official crowd: 26,921 at Etihad Stadium
