Their striker Anthony Modeste is three behind joint top-scorers Pierre-Emerick Aubameyang of Dortmund and Lewandowski, who each have 26 league goals, in the race to be top scorer.
Ancelotti made the case for video technology immediately after the game, saying the mistakes were unacceptable for the Champions League quarterfinals.
Real Madrid's Cristiano Ronaldo is challenged by Bayern Munich's Mats Hummels and Xabi Alonso at the Estadio Santiago Bernabeu stadium in Madrid April 18, 2017. Until he faced Bayern Munich.
The hat trick made him the first player to score 100 Champions League goals. "He always knows that when there's an important occasion, he's going to be there and he showed it again tonight".
Muller claims referee Viktor Kassai and his assistants disrupted the flow of the game with their questionable calls, during crucial periods of play for the Bundesliga champions - as Ronaldo appeared to scored two goals from offside positions.
In the Spanish league, Ronaldo's 19 goals leave him five behind Suarez and 10 behind Messi. "(Bayern president) Uli Hoeness and I, we've taken many blows.
Their joint retirements signal the end of an era at Bayern, with time also running out for veteran wingers Franck Ribery, 34, and Arjen Robben, 33, who both have contracts until June 2018. There are few players that are always there in the key moments, and the fans will be grateful for what Cristiano has done here.
After Robert Lewandowski had scored a 53rd minute penalty for Bayern, an own-goal by Madrid defender Sergio Ramos in the 78th had given the German side a 2-1 lead in regulation time, and sent the game into extra time.
"It's a special competition for Real Madrid", Ronaldo said. "I always give my best, and even when I don't score I'm trying to help the team".