The custody agreement was reached one week after Pique announced his imminent retirement from professional football and departure from FC Barcelona.
Bayern top Group C on 15 points, five ahead of Inter Milan who also reached the knockout stage after a 4-0 win against Viktoria Plzen, a result that eliminated Barcelona in the group stage for the second year in a row.
The defeat was another blow to Barca and manager Xavi Hernandez after they were left on the brink of Champions League elimination following a draw with Inter Milan last week.
The home win lifted Inter to second place in Group C on six points, three behind leaders Bayern Munich and three in front of Barcelona.
The Polish striker secured Barca's points in the 20th minute when he sped into the area, made a brilliant cut inside to clear a defender and slotted the ball to the goalkeeper's left.
For Bayern the win could not have come at a better time, following three consecutive draws in the Bundesliga.
Lewandowski, who came on as a substitute after the goal, continued his fine start to life in Spain with Barca's second 25 minutes from time to put the visitors in command.
The 3-0 win win over Sevilla lifts Barcelona to second place in the table on 10 points, two behind leaders Real Madrid who beat Real Betis 2-1.
Spanish newspaper El Pais said both the player and his wife Alysha Behague suffered minor injuries.
Real Madrid sit top of the table on nine points, level with Real Betis. Barcelona and Villarreal are right behind on seven points, with Osasuna and Real Sociedad on six.