The Ayrshireman finished joint third following a closing 67 at Alenda Golf in Alicante to book his spot in the six-round final, which starts on Saturday.
Also moving on to the final at Lumine Golf in Tarragona are Scott Henry, Daniel Young, Chris Robb, Duncan Stewart, James Ross and Craig Ross.
Henry, who finished joint second in the 2016 final, set up his chance to regain a main Tour card after tying for fifth at Desert Springs, where former South African Amateur champion Young also progressed.
Robb, the 2014 Scottish Amateur champion, also finished in joint fifth in his stage-two test at Las Colinas, where Stewart qualified as well after signing off with a 68.
For James Ross, it was mission accomplished at El Encin, where he finished joint 14th, while Craig Ross joined McDonald in making it through at Alenda Golf.
The hopefuls at Lumine will also include Marc Warren and Connor Syme after they finished outside the top 116 in this season’s Race to Dubai, as well as Calum Hill and Ewen Ferguson.
Among those to bow out at the second stage was Bradley Neil, who failed to secure an exemption for the final after finishing 190th on the main Tour money list this season.
l A brilliant eagle at the 16th helped Bryson DeChambeau claim his fourth PGA Tour title of the calendar year at the Shriners Hospitals for Children Open in Las Vegas.
DeChambeau trailed defending champion Patrick Cantlay by a single shot with three holes to play but he holed his 58-foot eagle putt from just off the 16th green to jump to 21 under par.
Former winner Martin Laird finished joint 28th, closing with a 68.