The Czech world number 35, who upset American second seed Emma Navarro in the semi-finals, avenged her Cincinnati first-round loss at the hands of Sun two weeks ago ahead of her US Open first round clash with 31st-ranked Yulia Putintseva on Tuesday.
Noskova got off to a solid start breaking Sun's first service game, only for the New Zealander to break back to maintain parity to force a tiebreak.
The teenager then saved two set points before clinching the opening set in over an hour.
In the second set Noskova capitalised on the New Zealander's unforced errors to break her serve again and hold a key advantage that secured her triumph in one hour and 58 minutes in the northern Mexican city.
"I was coming to this tournament not in the best mood, but it has changed a lot, it was such a great tournament for me," Noskova said.
"The circumstances and the opportunities I have had here, it was incredible for me and my career, really glad I won here and maybe I'll come back next year."
Despite the defeat, Sun, who grabbed the tennis world's attention after her Wimbledon quarter-finals run, will break into the top 50 for the first time before her US Open debut on Monday against Lucia Bronzetti.
"Thank you to my team, it was a great week for us. Even though I lost, it was a very good week," Sun said.