Wildcards Ebden and Gajdosova triumphed over unseeded Czech pair Lucie Hradecka and Frantisek Cermak 6-3 7-5 on Rod Laver Arena.
South African-born Ebden and Slovakian-born Gajdosova looked the stronger pair early on and then locked in an early break in the second set.
They had two break points on the serve of Fed Cup star Hradecka to go to a 5-2 lead but were unable to convert.
Instead the Czech duo grabbed that game and then broke Gajdosova to level the set at 4-4.
Cermak gave his team a 5-4 lead before Ebden squared the match again.
Hradecka then dropped her serve handing Gajdosova the opportunity to serve for the championship, which she did with relish.
She held a 40-0 lead with the Czechs clawing back to 40-30 before Cermak sent the ball long.
The Aussie duo, who were both first-round singles losers, were watched in the stands by Australian tennis legend Margaret Court, whose unmatched 62 major titles included 19 in mixed doubles.
Ebden's family has attended the Christian church run by Court in Perth since moving from South Africa to Australia when Ebden was about 12 and he considers her a tennis mentor.