The Spaniard has been heavily linked with a return to Athletic Club during this transfer window but still made a telling contribution for his current employees in Hungary on Thursday night.
The game took place in front of 20,000 watching supporters at the Puskas Arena in Budapest as part of a trial by UEFA.
Bayern were almost level midway through the first half, but Thomas Muller was denied a tap-in by the sliding Jules Kounde.
The rest of the evening was largely played out on Sevilla's half of the pitch, with Lewandowski having two goals disallowed after the break.
At the start of extra time, Neuer's large frame kept En-Nesyri out again, with his right foot tipping the Moroccan's shot on to the post.
Bono wasn't so impressive, though, in the build-up to Bayern's winning goal, parrying David Alaba's shot up in the air for substitute Martinez to nod in.