The result means that Rochdale now host the first leg and judging by his after match comments, manager Keith Hill was more than happy with that and none too concerned with the outcome of this particular game.
Both managers made changes ahead of more important meetings and the visitors almost scored in the opening exchanges but Nicky Southall was judged offside as he swept home Albert Jarrett's third minute cross.
Rochdale had a double opportunity in the 10th minute when first of all Will Buckley saw his effort hacked off the line and from the subsequent corner Jon Shaw saw his header meet the same fate.
It was the visitors who scored the only goal of the game though on 22 minutes when Curtis Weston ran virtually the length of the field to score. He appeared to have been fouled in the box by retreating defender Tom Newey but quickly got to his feet to stab the ball beyond home 'keeper Frank Fielding.
Either side of half time dangerous home winger Buckley saw efforts flash across the face of goal and captain Gary Jones saw his header graze the crossbar and a powerful drive deflected over the crossbar.
As the second half wore on Mark Jones saw his low free kick saved at the second attempt by Gillingham keeper Alan Julian and with time running out substitute Simon Ramsden saw his hooked effort brilliantly clawed away by the 'keeper.
The result means that Gillingham finish above Dale in the league but now face a further journey north this week for a much more important game that has the lure of a trip to Wembley at stake for both sides.