When did Square Taper Bottom Brackets retire from racing?
"First alternative" is a little tricky because if you looked hard enough you could potentially find a pro riding Sweet Wings cranks in the early 90s, which use a spindle and bottom bracket design thats very much a forebearer of external bearing cranks. And if you're not just talking road, you'd be able to find plenty of examples of MTB/DH and of course BMX riders riding Profile and other splined spindle tubular chromoly cranks also in the 90s. There were other 90s high end non square cranks too made by Bullseye and Tioga that could have found their way on to pro bikes.

Campy held out on ditching square taper for a long time. I want to say Ultra-Torque wasn't released until 2007 and before then all their cranks were ISO square. I would suspect the last square cranks in the peloton were on all-Campy bikes.