Putnam closed with a 2-under 68 to match Baker (66) at 13-under 267 at Panama Golf Club.
The 28-year-old former Pepperdine player earned $112,500 to take the money lead with $171,100. The top 25 at the end of the regular season will earn PGA Tour cards for next season.
Putnam also won the 2014 WNB Golf Classic. He finished in the top 11 in his first three starts this season, tying for eighth and 11th in the Bahamas and finishing fifth last week in Colombia.