Matthew Lund, Ian Henderson and Peter Vincenti scored the goals for the League Two leaders as they registered their fourth straight victory, while Portsmouth lost their third consecutive game as they continue to battle against relegation.
Although Rochdale and their visitors on Tuesday are separated by 20 positions in the table, the home team's manager Keith Hill said his players had negotiated a tricky fixture against a side he rates highly.
"I think it's testament to the squad ... and the belief that they have in each other that we can perform like that against, what I do consider, a very good side with quality players, who are probably suffering from a lack of confidence," Hill told Rochdale's website.
"So it was a very dangerous game for us tonight and I thought we managed the game exceptionally well."
Lund gave Hill's side the lead in the 16th minute at Spotland Stadium with a close-range header, while Rochdale doubled their advantage just before the hour-mark when Henderson converted after latching onto a long ball.
Vincenti scored the hosts' third goal in the 63rd minute from Matt Done's cross, as Rochdale extended the visitors' winless streak to six matches.
A brace from Darren Carter had put Northampton in front at home but the visitors from Wimbledon ruined the hosts' night when Luke Moore scored in the sixth minute of second-half stoppage time.
Third-placed Chesterfield stayed within three points of Rochdale after edging out Morecambe 1-0 thanks to James O'Shea's 19th-minute goal.
It was the sixth consecutive win for Nigel Worthington's men with William Hayhurst scoring in the 11th minute for York.
