An away goals defeat to Atletico Madrid, despite a 2-1 win in Germany on Tuesday, sealed Bayern's elimination from this season's competition and ended Guardiola's hopes of going out on a European high.
The Spaniard arrived at Bayern following their 2013 treble-winning season, but rather than tighten their stranglehold on the continental competition, he has always fallen at the last four, each time against a different Spanish side.
"That is football. You can play better and still be eliminated," said Guardiola, who will move to Manchester City next season.
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"I feel sorry for my players because they deserved the very best."
Guardiola, who had won 14 titles in four years at former club Barcelona, including two Champions League triumphs, would not be drawn into analysing his record at Bayern, who can win a record fourth consecutive Bundesliga title this week.
"We missed one more goal in the game today. That was all. We played the game we wanted, did it well but it was not enough. It hurts, of course. Every time it hurts. But my track record in Munich is not up to me to decide," he said.
"I was very happy here. I worked for the players, not for a track record."
His players, who won the Champions League before Guardiola arrived in 2013, were equally disappointed.
"There is no point in thinking about what happened last year (against Barcelona) and the year before (against Real Madrid)," said Bayern captain Philipp Lahm.
"Sadly we did not give our coach a big reward today and say goodbye to him in the way we wanted."
Bayern looked on course to reach the final after Xabi Alonso's deflected free kick cancelled out the Spanish side's 1-0 lead from the first leg.
Yet a goal from Antoine Griezmann was enough to send Atletico through even though Bayern's Robert Lewandowski scored in the 74th minute to seal a 2-1 win on the night.
Bayern's Thomas Mueller missed a penalty when they were leading 1-0 while Atletico's Fernando Torres also had an 84th-minute spot kick saved.
"We made a lot of things right and only a few things wrong," Mueller told reporters.
"But those few wrong things were enough. We are very disappointed. I just don't have words to describe this now. It is more painful than the previous two years."
(Reporting by Karolos Grohmann; Editing by Toby Davis)
