Oxford remain in the play-off places despite failing to win for the third home game in a row.
Gillingham were indebted to keeper Paulo Gazzaniga, who produced a superb one-handed save from Asa Hall's well-struck shot on the turn.
Liam Davis saved Oxford with two last-ditch blocks, first denying Danny Kedwell and then Jo Kuffour.
Hall went close again but his fierce half-volley was headed off the line by Matt Fish.
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Gillingham manager Andy Hessenthaler told BBC Radio Kent:
"We're still where we were, four points away and we're relying on other teams to slip up but it's not over.
"We worked our socks off and I can't ask anything more of my players.
"The only thing I'm disappointed with is our quality in the final third. If we'd found that maybe it would have been a different game."