Inter Milan sinks Bayern Munich, 3-2

Staging one of the great comebacks in European Champions League history, defending champion Inter Milan scored with only minutes remaining to defeat Bayern Munich, 3-2, in Germany on Tuesday night to advance to the quarterfinals of the continent’s most prestigious soccer tournament.

A goal by Macedonian forward Goran Pandev off a pass from Cameroon striker Samuel Eto’o in the 88th minute made all the difference, tying the series, 3-3, on aggregate and allowing the Italian champions to go through on the away-goals rule.

Bayern Munich had won the first leg in Milan, 1-0, and had rallied to lead, 2-1, in the second leg before the roof caved in on the German team’s season.

Already knocked out of the German Cup and all but mathematically eliminated from winning the Bundesliga title, Bayern Munich’s last opportunity to earn any silverware this season lay in the Champions League.

A beaten finalist last season, when Inter Milan won the title in Madrid, Bayern Munich seemed poised to go through to the quarterfinals. But it was left to rue a handful of wasted scoring chances, particularly in the first half when it was the dominant team.

Lame duck Coach Louis van Gaal, who had agreed to leave at the end of the season, now might be departing even earlier.

“It’s not the first time this has happened,” the Dutchman said. “Four or five times already this season we have given away a match we should have won, and today it happened again.”

In Tuesday’s other round-of-16 game, Manchester United rode two goals by Mexican striker Javier “Chicharito” Hernandez to a 2-1 victory over Olympique Marseille of France in Manchester to secure a quarterfinal spot for the fifth consecutive season.

But it was the game in Munich, in which both teams’ fortunes swayed back and forth, that had neutral fans worldwide glued to their television sets.

“It’s a great moment, a fantastic joy, and I can only thank God for letting me experience this feeling tonight,” said Inter Milan’s Brazilian coach, Leonardo.

“It’s a historic result considering how difficult the game was and how strong our opponents were.”

Leonardo said Pandev’s late goal was a fitting reward for his players’ belief.

“It’s a sign that these players have great faith in the team, we never give up,” he said. “The European champions are still standing.”

Inter Milan took the lead in the fourth minute on a goal by Eto’o, but although that rocked Bayern Munich and tied the series, 1-1, on aggregate goals, it spurred a great response from the German team, a four-time European champion.

Bayern Munich tied it up in the 21st minute on a goal by Mario Gomez, who took advantage of an error by goalkeeper Julie Cesar, who allowed a shot by Arjen Robben to bounce free off his hands and chest.

Ten minutes after Gomez’s goal, Bayern Munich went in front when Thomas Mueller scored.

Bayern Munich held onto the lead until the 63rd minute, when Wesley Sneijder scored off a pass from Eto’o.

Bayern Munich defenders failed to close down Eto’o as he made a run across the top of the penalty area and the Cameroon star slipped a pass to the unmarked Pandev, who did the rest.

“I’m so happy for Pandev, who has had a very difficult period,” Leonardo said. “He has been criticized for missing a few chances but he has always continued to work hard and he has been repaid tonight.”

Inter Milan also has been rewarded for its effort and joins Barcelona, Shakhtar Donestk, Tottenham Hotspur, Schalke’04 and Manchester United in the competition’s last eight.

The last two quarterfinalists will be determined Wednesday when Chelsea plays host to Copenhagen and Real Madrid is at home against Olympique Lyon.

Manchester United’s passage was relatively easy, with the English Premier League leader taking the lead in the fifth minute at Old Trafford when Hernandez was presented with the easiest of scoring chances by an incisive pass from Wayne Rooney.

Hernandez was on target again in the 75th minute, this time scoring off a pass from Ryan Giggs, and all that kept Olympique Marseille in the hunt until the end was an 82nd-minute own goal by defender Wes Brown.

The teams had tied, 0-0, in France.

“The partnership between Wayne and Javier is developing well,” said Manchester United Coach Alex Ferguson. “Where Wayne’s been playing in the last couple of games, he’s a real threat because he’s got such power and speed with the ball. Hernandez is unbelievable, his movement: for the goal; in, out, in, out.”

Marseille Coach and former France World Cup winner Didier Deschamps said his team’s inability to finish its chances was ultimately to blame for the defeat.

“I think we missed an opportunity because we had the chances,” Deschamps said. “There are regrets.”

grahame.jones@latimes.com