The Barons posted their second consecutive victory over a Maryland-based USL Second Division club thanks to a 108th-minute penalty kick by JT Noone.
They knocked out Crystal Palace Baltimore 3-0, a week earlier.
Five USL1 and two USL2 teams also advanced to the third round, entry point for MLS's eight representatives.
The game of the evening was a battle of North Carolina teams. USL2's Wilmington Hammerheads beat USL1's second-place Carolina RailHawks in a shootout after their game ended in a 3-3 tie.
The fourth goal of overtime was scored by visiting Wilmington's Kenny Bundy in the 120th minute.
Real Maryland Monarchs (USL2) 0 Ocean City Barons (PDL) 1 (Noone pen. 108) (OT).
Rochester Rhinos (USL1) 2 (Heins 82, Bertz 113) Cleveland City Stars (USL1) 1 (Stewart pen. 59) (OT).
Carolina RailHawks (USL1) 3 (Diallo 34, Plotkin 98, Glinton 118) Wilmington Hammerheads (USL2) 3 (Bagley 22, Karalexis 92, Bundy 120) (OT).
(Wilmington Hammerheads win 4-3 on penalty kicks.)
Harrisburg City Islanders (USL2) 0 Western Mass Pioneers (USL2) 0 (OT).
(Harrisburg City Islanders win 4-3 on penalty kicks.)
Miami FC Blues (USL1) 0 Charleston Battery (USL1) 1 (Hemming pen. 65).
Minnesota Thunder (USL1) 4 (Saint-Preux 23, Cvilikas 39, Tarley 78, 82) Chicago Fire Premier (PDL) 0.
Austin Aztex (USL1) 2 (McMahen 45, O'Brien 48) El Paso Patriots (PDL) 0.
Sonoma County Sol (USASA) 0 Portland Timbers (USL1) 3 (Josten 7, Keita 87, 90).
June 30-July 1
Harrisburg City Islanders (USL2) at New England Revolution (MLS)
Ocean City Barons (PDL) at D.C. United (MLS)
Chicago Fire (MLS) at Wilmington Hammerheads (USL2)
Chivas USA (MLS) at Charleston Battery (USL1)
Columbus Crew (MLS) at Rochester Rhinos (USL1)
Kansas City Wizards (MLS) at Minnesota Thunder (USL1)
Houston Dynamo (MLS) at Austin Aztex (USL1)
Seattle Sounders (MLS) at Portland Timbers (USL1)