Luke Moore's late equaliser, just seven minutes after coming on as substitute, left Wanderers supporters waiting for the outcome of games at Blackburn and Portsmouth.
Finally, news filtered through that Reading and Pompey had only drawn and, for only the second time in their history, Bolton will kick-off in Europe in 2007-08.
It would have been cruel on Lee had his side missed out. Thrown in at the deep end after the departure of Sam Allardyce, 'Little Sam's' task was a thankless one.
But he and his players bounced back from the mauling at West Ham United to clinch seventh place.
Just how many of those players will still be at the Reebok in August remains to be seen.
Former boss Sam Allardyce accepted chairman Phil Gartside's invitation to watch the game from the directors' box.
And he saw player-coach Gary Speed give Bolton the lead before Craig Gardner smashed in a superb volleyed equaliser after John Carew's flick on.
Both sides were forced to make changes at half-time as Nicolas Anelka gave way to Idan Tal and Villa replaced injured keeper Thomas Sorensen with Stuart Taylor deputising.
And Taylor was soon picking the ball out of the net as Kevin Davies scored his fourth goal in eight games.
Davies wrong-footed Aaron Hughes before firing in left footed from eight yards.
Kevin Nolan should have sealed the win but failed to hit the target. Moore came on to replace Patrik Berger in the 74th minute and it proved an inspired substitution by Martin O'Neill.
After Bolton failed to clear their lines Ashley Young crossed from the right and Moore blasted in his fourth goal of the campaign.
That was the end of the scoring but not the end of the drama.
But Bolton will be in Europe though recent performances suggest they are fortunate to be there.