Gordon Strachan's side avoided the wooden spoon by completing a surprising double over Igor Stimac's men, with the Norwich and Everton attackers netting for the hosts.
Robert Snodgrass opened the scoring, just as he did in Zagreb in June, before Steven Naismith rifled in Barry Bannan's saved penalty to ensure Scotland's continued progression under Gordon Strachan.
The Norwich forward had joined up with the squad late after his partner gave birth to daughter Leonie last week, but he showed no signs of tiredness as he rose highest to head home the game's opening goal in the 28th minute.
Naismith grabbed Scotland's second with 17 minutes left, netting the rebound after Bannan's spot kick had been saved to wrap up the win for Strachan’s fast-improving side.
The win meant that Scotland leapfrogged Wales in Group A, while Croatia finished in second to take one of the eight playoff places.
Strachan made three changes from the side that won 2-1 in Macedonia last match, bringing in Allan McGregor, James Morrison and Snodgrass for David Marshall, Steven Whittaker and Shaun Maloney.
Croatia manager Igor Stimac, meanwhile, made four changes to the side that lost 2-1 in Belgium on Friday, including captain Darijo Srna, who returned from suspension. QPR midfielder Niko Kranjcar, who came off the bench to score against Belgium, was also among the inclusions.
The visitors started much the better side and their early pressure was nearly converted into a goal 12 minutes in, but former Blackburn Rovers striker Nikola Kalinic just failed to get on the end of an excellent Srna cross.
Scotland's first chance fell to Naismith, but the Everton man shot over from 18 yards after Scott Brown's initial effort had been blocked.
Strachan's men improved as the half went on and they took a deserved lead after 28 minutes when Snodgrass, scorer of the winner the last time these sides met, leapt above Vedran Corluka to head home Charlie Mulgrew's cross.
And the Norwich striker nearly grabbed a second a few minutes later when Brown slipped the ball into his path as he raced through on goal, but Croatia goalkeeper Stipe Pletikosa made an excellent save down to his left.
Mario Mandzukic had a chance to equalize shortly before halftime but he volleyed into the ground and over the crossbar when another Srna cross found him free at the back post.
The second half was a scrappy affair with few chances, with Luka Modric's long shot, which McGregor saved easily, the only one of note.
The Croatia fans responded to the lull in incident with some entertainment of their own, letting off a series of flares that left the pitch covered in smoke.
Stimac brought on Eduardo for Kalinic in search of some inspiration with time running out and he almost provided it when he latched onto a through ball and rounded McGregor, but the former Arsenal man finished into the side netting from a tough angle.
And Scotland punished that profligacy soon after when the dangerous Ikechi Anya was felled by Domagoj Vida inside the area.
Bannan's penalty was saved well by Pletikosa initially, but Naismith reacted quickest to fire home and seal the victory for Strachan's side.