The best that I can find is a page on the Wayback Machine, that shows a prototype of the Dura Ace 7700 groupset (first to have the splined cranksets) being given to several teams and individuals for the 79th Giro d'Italia, as well as being used for several races later in the year (Including the Olympics with a win) (emphasis mine):
Dura-Ace took another leap forward with the appearance of the new 9-speed 7700-series components. 300 production prototype groups were prepared for the Mapei, Polti, TVM, Panaria, MG, and Festina teams who would begin testing the components in the 79th Giro d’Italia. After three weeks grueling weeks of racing, the 7700 components successfully completed their first test under fire.
Later in the year, when Pascal Richard won the Olympic Road Race, the top 12 places were all riding on prototype 7700!
Johan Museeuw several months later with the first World Professional Road Championships won on Shimano’s new ultra lightweight 9-speed. In addition to Museeuw’s win, Shimano sponsored riders took the top 9 spots riding Dura-Ace 7700 series equipped bicycles.
And of course, the first TdF win for Shimano was 1999 with Lance Armstrong.
As far as the last time they were used in pro racing, I cannot find a definitive date. Since Shimano patented the Octalink design, which led to the creation of the 10 splined ISIS system, I would suspect that it would have been whichever groupset adopted ISIS last, or possibly some of the lesser funded Continental/USA teams clinging to fading technology for budget reasons.