Despite the win, Bayern Munich still have work to do in Europe, with this season's Champions League final on home soil.
Atletico have now won just one of their last 10 Champions League away matches.
Sporting Lisbon will face Porto in the Portuguese Cup final on May 26, aiming to secure a double.
Benjamin Bourigeaud scored a hat-trick for Rennes, including a pair of penalties, but goals from Luka Jovic and Rafael Leao ensured Milan were never really in danger of blowing a 3-0 lead from the first leg.
Manchester United crashed to a second successive Champions League defeat on Tuesday, losing 3-2 at home to Galatasaray, while Lens stunned Arsenal 2-1.
Portugal attacker Goncalo Ramos has joined Paris Saint-Germain from Benfica on a one-year loan deal with an option to buy
The 35-year-old World Cup winner left Juve as a free agent last month amid claims he could be targeted by a club in Saudi Arabia.
Inter had come into Wednesday's clash in a miserable run of form in which their only win in their last eight games had come in last week's first leg in Portugal.
Nicolo Barella and Romelu Lukaku scored as Inter Milan defeated Benfica in UEFA Champions League.
Holders Real Madrid will play Chelsea in the quarter-finals of the Champions League while Manchester City were drawn against Bayern Munich on Friday
The UEFA Champions League quarter-finals draw will be held on Friday at 4:30 PM IST. Real Madrid, Bayern Munich, Manchester City and Napoli are among the favourites to go through.
Goncalo Ramos produced two clinical finishes either side of half-time to ensure the two-time European Cup winners would reach the quarter-finals in consecutive seasons.
Club Brugge face Benfica in a Champions League Round of 16 match.
Chelsea paid a Premier League record fee of 121 million euros to sign Enzo Fernandez as Joao Cancelo made a surprise move to Bayern Munich and Jorginho joined Arsenal on a frantic transfer deadline day in Europe.
AC Milan reached the Champions League knock-out stage for the first time in nine years on Wednesday with a 4-0 victory over Salzburg, while RB Leipzig also qualified by thrashing Shakhtar Donetsk
Juventus were knocked out of the Champions League in the group stage for the first time in nine years on Tuesday but Chelsea, Paris Saint-Germain, Benfica and Borussia Dortmund all secured qualification for the knockout stage with one group game to spare
Real Madrid and Manchester City both found the going tough in the Champions League group stage on Tuesday night but battled through to draws that were enough to qualify for the knockout stages
Lionel Messi suffered a slight calf issue in last week's 1-1 draw in Portugal and missed Saturday's draw at Reims in Ligue 1.