After Maya Yoshida had cancelled out Mame Biram Diouf's opener, the visitors looked favourites for the three points before Crouch poked in from close range to earn Stoke just their second Premier League win of the campaign.
Stoke have struggled for goals in the first half of games this season but it took just two minutes for the home side to get an effort on goal with Joe Allen blazing over from distance.
Virgil van Dijk - who was making his first Southampton appearance since January 22 - made a couple of timely blocks during the early stages but Stoke continued to dominate without ever threatening to trouble Fraser Forster.
On the quarter-of-an-hour mark, Xherdan Shaqiri eventually worked the Saints stopper after a sharp turn, but the visitors finally began to make some inroads at the other end.
Just before the half-hour mark, Eric Maxim Choupo-Moting brought an excellent save out of Forster but Stoke finally took the lead just before the interval when Biram Diouf powered in a free header for just his second goal since the start of the last campaign.
Two minutes later, Stoke should have doubled their advantage when Saido Berahino was fouled by Van Dijk inside the penalty area, but the forward - without a goal in 31 matches - saw his attempt saved by Forster, his first from 12 yards in a Southampton jersey.
After the restart, Stoke picked up where they left off with Geoff Cameron having a speculative shot saved by Forster, but the Saints soon changed the momentum of the contest and dominated for large parts of the second half.
Twice in the space of four minutes, Long squandered two good opportunities with his head, before Van Dijk also sent a header off target as the visitors began to take the aerial approach.
Stoke threw on Crouch in an attempt to aid with defensive set pieces and to hold the ball up in attack, but his introduction did not prevent Southampton from deservedly getting on level terms.
After Long had miscued his strike from a corner, the ball fell for Yoshida who directed the ball into the net via the underside of the crossbar.
Southampton remained in the ascendancy but with five minutes remaining, Crouch came back to haunt his former club with a finish from close range after Southampton had failed to clear inside the penalty area.
During five minutes of added-on time, Manolo Gabbiadini, Charlie Austin and Long all sent clear-cut chances wide of Butland's post, and it ensured that Stoke could finally get another top-flight win on the board after having to wait since the second weekend of the season.