As Matías Giménez stepped up to take Olimpia's fifth penalty, Cuca, the Atlético Mineiro coach, knelt on the touchline. Clad in jeans and a T-shirt, he rocked back and forth, head bowed, arms crossed over the sequined pattern on his chest. He didn't look as Giménez's shot struck the top of the post. The noise of the crowd told him the kick had been missed and he pitched forward, to lie still for a second or two before being engulfed by his celebrating coaches: Atlético, after another unlikely comeback, were Libertadores champions for the first time.

The Olimpia defender Herminio Miranda had given Atlético the initiative, his kick, the first of the shootout, being easily kicked away by Victor, who had managed to encroach three yards or so from his line without being punished by the Colombian referee Wilmar Roldán. It wasn't the misses from Miranda and Giménez that were decisive, though; it was two earlier mistakes, a defensive gaffe from Wilson Pittoni and an extraordinary miss from Juan Carlos Ferreyra that allowed Atlético back into the game. Well as the Brazilians played, at least after half-time, Olimpia were responsible for their own downfall. So devastated were they that, despite the generally tetchy mood, they could not even raise themselves for the traditional Libertadores final punch-up, although there was a brief altercation with a tubby fan who invaded the pitch.

Leading 2-0 from the first leg, the Paraguayans, who would have become the fourth most successful side in Libertadores history with a win, seemed to have done everything right in the first half. Although Diego Tardelli flashed a ball across the face of goal and Ronaldinho drew an awkward save from Martín Silva with a 25-yard drive in the opening minutes, the storm soon blew out and their back three looked increasingly assured as the first half went on.

Only the left-sided Alejandro Silva in Olimpia's midfield had licence to attack and, accordingly, Atlético's only consistent threat came from the forward surges of their right-back Michel. Twice, though, Olimpia almost capitalised on the space left by his attacking. Juan Manuel Salgueiro laid in Fredy José Bareiro with a deft flick with the outside of his boot after 16 minutes, only for the forward to snatch at the chance and scuff his shot straight at Victor. Silva did rather better when Bareiro slid him through 11 minutes before half-time, cutting inside on to his right foot, but his low drive was saved by Victor.

But then, 45 seconds into the second half, came the first decisive moment. Ronaldinho, on the right, looked outside as though to slip a pass wide and hooked a no-look cross into the box. Whether the subterfuge fooled anybody is difficult to say but Pittoni, under little pressure, fluffed his clearance. Jô, the former Manchester City and Everton forward, pounced to hook the ball home, and Atlético Mineiro, in the first minute of the second half, had a lifeline and the tone of the game was changed.

Pittoni's gaffe inspired Atlético, so often recently the masters of late drama, and awoke panic in Olimpia. The second half descended into anxious, compelling drama. A Tardelli shot was beaten away by Martín Silva, then Jô turned superbly only to hit his snap shot straight at the keeper. A dropping header from Tardelli bounced away off the face of the bar and Júnior César, roaming forward from left-back, was another to hit his shot into the body of Martín Silva.

If the keeper had been fortunate that forwards kept striking the ball straight at him, though, his save from Leonardo Silva after 71 minutes was simply superb. The defender's header from Ronaldinho's clipped free-kick wasn't entirely clean, and the slight loss of pace proved decisive as Martín Silva scrambled across his goal to paw clear. His save from Ronaldinho's deflected drive with 10 minutes remaining was even better, twisting back to his right to parry – although, as it turned out, it was needless, Tardelli having been flagged for offside as the initial shot cannoned off him.

And then, with seven minutes remaining, Olimpia made their second key error. Giménez lofted a perfectly weighted ball over the top of the Atlético backline for the substitute Ferreyra. He nudged the ball past Victor as the keeper charged from his goal and seemed to have the easiest of tasks to win the game: an open goal from 25 yards out. As he checked back on to his right foot, his left foot slipped from under him and he was left flailing, alone on the turf a vital yard from the ball.

Two minutes later came the red card that had seemed likely throughout the second half after Júlio César Manzur, already booked for a crude lunge on Ronaldinho, cynically blocked Alecsandro. Ronaldinho whipped the free-kick into the wall and it seemed Atlético's chance might have gone, but Olimpia never fully cleared and as the ball was crossed from the right Leonardo Silva looped a header across the face of goal and in at the far post.

From then on it seemed just a matter of when. Rever headed against a post, Martín Silva made another fine save from Ronaldinho and then tipped a Josué shot over, and Alecsandro dinked a shot over the keeper only for Herminio Miranda to head away. It's 26 years, though, since the last goal in extra time in a Libertadores final and, for the seventh time in the last 14 years, the tournament was settled on penalties.

Ronaldinho, still only 33, would have taken Atlético's fifth kick. He has been exceptional at times this year, the creative hub of a side that has produced the best football in the competition. He was denied the climax of converting the winning penalty, but joins Cafu, Dida, Roque Júnior, Carlos Tevez and Walter Samuel in the select group to have won both the Champions League and Libertadores.

But this was less a triumph about individual milestones than about a team that relied so often on late drama it came to believe in its own destiny, attacking and attacking until eventually Martín Silva was beaten.