Tom Hopper and Anthony Scully were on target as City recorded their first league win of the season, stretching their unbeaten start to the campaign to five matches in the process.
Both City's goals came in the first half as Mark Kennedy's side turned on the style, with Cameron Brannagan pulling one back for the hosts after the break.
Karl Robinson's men pushed for a leveller, but the Imps dug deep and battled hard in the Oxfordshire rain to ensure three points.
Attendance: 6,912 (326 away)
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