Vaughan, whose lone goal in the 52nd minute gave Guyana a 1-1 draw with Curacao on Wednesday, scored in the 61st minute of Sunday's encounter with Anguilla after Ursuline Primus put the Guyanese ahead in the 38th.
The victory finished Guyana atop Group C with four points, one better than Anguilla, which beat Curacao 2-1 on Friday.
Guyana joins the Bahamas in the second round of Caribbean qualifying. Group D in San Cristobal, Dominican Republic, begins play Wednesday with the host, Jamaica and Aruba. A schedule for Group A between Dominca, St. Kitts & Nevis and Trinidad & Tobago has not yet been determined.
The four group winners will face off in a second group stage, from which three teams will qualify for next year's CONCACAF finals.