Fourth in the pool heading into a crunch clash in Cardiff after a slow start to the campaign, Ryan Giggs' men suffered another setback on Monday (AEST) as it trailed to Nikola Vlasic's early goal.
Gareth Bale struck shortly before half-time to lift Wales, yet they could not get the crucial second goal and were forced to settle for a point.
Wales now requires a helping hand from opponent Croatia when it faces Slovakia, with the FIFA World Cup finalist itself still to secure a place at the finals after failing to win here.
Croatia took control from the outset and had to wait just nine minutes for the opener, with Josip Brekalo dancing in from the left and Bruno Petkovic teeing up Vlasic to shoot low past Wayne Hennessey via the left-hand post.
Only a stunning, stooping Hennessey save denied Ivan Perisic a quick second with a 12-yard header, although a stoppage for Dan James to receive treatment for an apparent head injury slowed the visitors' momentum.
Wales continued to toil until the vital equaliser arrived from a predictable source three minutes into the consequent added period, as Ben Davies picked out Bale to fire beyond Dominik Livakovic.
The home side improved after the restart but chances was at a premium, with only a shaky Livakovic fumble from James' drive offering the Welsh fans any real excitement in front of goal.
A combative match took its toll in the closing stages, too, as Luka Modric was substituted with an injury and Bale ended the contest hobbling badly.