Flesch picked up his second win on the PGA Tour and jumped up 20 spots from last week.
Tiger Woods remains in first place, followed by Vijay Singh, Ernie Els, Davis Love III and Masters champion Phil Mickelson.
Mike Weir held on to sixth, followed by Jim Furyk, whose wrist injury has apparently not healed enough for him to defend his U.S. Open title next month. Padraig Harrington, who came in second at the Deutsche Bank - SAP Open TPC of Europe, stayed in eighth.
Chad Campbell finished second at the Colonial and climbed four notches to ninth. Retief Goosen rounded out the top 10 for another week.
Kenny Perry dipped two to 11th, while Australians Stuart Appleby and Adam Scott each fell one to accommodate Campbell's move. Darren Clarke and Scott Verplank maintained their spots from last week.
David Toms came in 16th, followed by Byron Nelson champion Sergio Garcia. Nick Price moved up two to 18th and Jonathan Kaye dropped one to No. 19. K.J. Choi also fell one to complete the top 20.
Trevor Immelman collected his second win of the season at the European Tour's Deutsche Bank - SAP Open TPC of Europe. The victory moved the 24-year-old South African up 21 spots to 32nd.