The German side score seven for the second successive game, while Marseille leave it late to get past Inter Milan to reach quarter-finals for first time since 1993.
Rampant Bayern Munich crush Basel in Champions League
Mario Gomez scored four goals as Bayern Munich marched into the Champions League quarter-finals by smashing Basel 7-0 in the second leg of their last 16 clash.
It was their biggest win in a Champions League knockout match as records tumbled in Munich and Bayern bettered their 7-1 home win over Sporting Lisbon from the 2009 competition, also in the round of 16.
Having come to Germany holding a 1-0 lead from the first leg three weeks ago, Basel's dreams of reaching the Champions League's last eight for the first time were rudely awakened as they lost the tie 7-1 on aggregate.
Bayern coach Jupp Heynckes hailed his team's 'perfect' performance as they have now scored 14 goals in their last two games. "We had already played well last Saturday and I noticed this week how much the team wanted to go through to the next round," he said after his team also smashed Hoffenheim 7-1 last Saturday in the German league.
"Today, we have put in a top class performance from the first until the last minute. Overall, it was a perfect game from us."
Having netted a hat-trick against Hoffenheim, Gomez scored four more, while Dutch winger Arjen Robben again scored twice against Basel. "It was fun to play in that. To score seven goals in a Champions League match speaks for itself," said Robben.
"Fourteen goals in our last two games after our defeat at (Bayer) Leverkusen speaks volumes for the way we have played."
Thomas Mueller scored the other Bayern goal.
Elsewhere, substitute Brandao scored in injury time to send Marseille into the last eight of the competition for the first time since winning the competition in 1993 as they ousted Inter Milan.
Inter won the second round, second leg match 2-1 at the San Siro after a hectic finish in which Marseille goalkeeper Steve Mandanda was sent off giving away a penalty even later in injury time.
Giampaolo Pazzini, who was brought down by Mandanda, dispatched the spot-kick with the last kick of the match to give the Italians victory but they still went out on away goals.
Diego Milito had earlier given Inter the lead 15 minutes from time and the match looked to be heading into extra-time until the eventful three minutes of injury time.
Almost everything in this last 16 tie happened in injury-time with Andre Ayew giving the French victory in the first leg three weeks ago with a last-gasp goal at the Stade Velodrome.
Marseille coach Didier Deschamps was understandably elated.
"I'm very happy because we've had a happy ending, it's emotional," he said.
"We had a really top quality team in front of us and it's true that Mandanda kept us afloat in the first half.
"We conceded 15 minutes from time but it probably didn't change anything, we knew we could concede because we needed to score.
"We've had a difficult period recently but the noise made by the people who came here made me very proud."
Inter coach Claudio Ranieri may well be searching for a new job after this defeat with his team out of contention for silverware and facing an uphill battle in the league just to qualify for Europe next season.
Ranieri blamed defeat on a lack of luck.
"Over 180 minutes Marseille had three shots on goal but in football the team who wins is the one that scores, so well done to them," he said.
"This year we haven't had any luck, I can't ask the team for more."