The 34-year-old South African has been a crowd favourite in his four seasons with Ulster and is retiring at the end of the season.
But the 22-20 defeat to Leinster ensured Muller's - and Ulster's - season was extended after securing a RaboDirect PRO12 play-off place.
Paddy Jackson scored all of Ulster's points in the loss which means the two sides are likely to meet again at the RDS in the last four.
"It was bittersweet, we so dearly wanted to win that game," said Ulster captain Muller.
"I want to say a massive thank you to every single person in the crowd and at home as well, the support me and my family have been given has been out of this world.
"To lose the game by two points, like we did against Saracens, against a side that has won the European Cup three times in the last few years is a brilliant performance.
"It shows the character of the team, but it doesn't make it any easier, it's still another loss.
"The funny thing is we're in the semi-final with it and we'll see them again in the semi-finals again so we're excited for that."
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