The Bayern manager made seven changes to his starting line-up on Saturday, leaving out key players Harry Kane, Luis Diaz and Michael Olise.
Despite the risk, Bayern delivered one of their most convincing performances of the season, extending their perfect Bundesliga start to nine straight wins.
Speaking after the match, Kompany said the decision was part of a long-term strategy to keep his players fresh with a demanding schedule that includes Tuesday's Champions League clash against Paris Saint-Germain.
"Of course we're always stronger when Harry plays and is in top form," Kompany said. "But today felt like the right time to let others step in. Everyone keeps asking when Harry or Lucho will get a rest, well, today was that day. And now we have a rested Harry for PSG."
The Belgian also praised his squad's professionalism, revealing that the senior stars supported the plan. "They are all top professionals. Whether it's Harry, Diaz or Olise, they fully understood the situation. They know the demands we're facing," he added.
Kompany admitted that making seven changes was a risk but said he was delighted with how his players responded. "Many thought things could go wrong today, maybe even our opponents. But we wanted to go at it with full intensity.
"It can be dangerous, but you build a squad for moments like this."
The victory kept Bayern firmly in the Bundesliga title race, while attention now turns to their showdown with PSG, where Kane and Diaz are expected to return to the starting line-up.
Bayern Munich have made a blistering start to the 2025/2026 season under head coach Vincent Kompany, whose side have rewritten European football history with a remarkable 16-game winning streak.
Real Madrid's hierarchy are growing uneasy over the team's sudden dip in form but remain confident that head coach Xabi Alonso can restore balance after a turbulent fortnight.
Arne Slot believes Liverpool's toughest spell of the season is now behind them, with a crucial run of winnable fixtures offering a chance to reignite their campaign after a heavy defeat to Manchester City.
Germany coach Julian Nagelsmann has urged Bayern Munich's 17-year-old talent Lennart Karl to focus on development with the under-21 side before thinking about a senior national team call-up.
