New York's decision to option three players comes as roster sizes had to be reduced from 30 to 28. The team has one open spot to fill.
Per MLB.com's Bryan Hoch, Yankees manager Aaron Boone said he won't rush Aroldis Chapman back as he was recently cleared to return after being diagnosed with COVID-19.
None of the players has seen much playing time for the Yankees so far this season.
Andujar is the biggest name of the group that was moved to the alternate site. The 25-year-old finished second in American League Rookie of the Year voting in 2018 but is working his way back after having surgery last May to repair a torn labrum that limited him to 12 games in 2019.
With Gio Urshela locked in as the starting third baseman, Andujar had just one hit in 14 at-bats in five games.
Nelson allowed seven runs (six earned) in 1.2 innings of relief against the Phillies in the first game of Wednesday's doubleheader.
Estrada has gone 2-for-2 in two games off the bench. He recorded his first RBI of the season in the seventh inning of the Yankees' 11-7 loss to the Phillies on Wednesday.