The Bayern Munich star had been tied with Cristiano Ronaldo as the section's top scorer on 15 prior to his side's final Group E game against Montenegro, where it needed a point to progress.
Poland saw off a spirited fightback from the visitor to win 4-2, with the third home goal - five minutes from the end - coming from Lewandowski.
That strike made the 29-year-old the first player to hit 16 in a single campaign of either the UEFA section of World Cup qualifying or the European Championship equivalent.
Behind Poland, Denmark booked a play-off spot with a 1-1 draw against Romania in Copenhagen.
And Northern Ireland is also assured of a place in November's crunch play-off fixtures, with Slovakia's leapfrogging of Scotland in Group F meaning Michael O'Neill's men can no longer finish as Europe's worst pool runners-up.
Slovakia, by contrast, must wait to see how Wales and Croatia fare to see if they will join Denmark and Northern Ireland in the draw.