Pompey dropped to eighth in the League One standings following a disappointing defeat at struggling Swindon.
Brett Pitman bagged a brace against his former club in the 3-1 County Ground loss, with the second coming from the penalty spot following a challenge by Charlie Daniels.
Ronan Curtis did reduce the deficit for Danny Cowley's men, but they were unable to find a leveller before Tyler Smith wrapped things up in stoppage-time.