Lee Sinnott's side were by far the best of the two relegation-haunted teams at the Alexandra Stadium.
Their passing was crisper and their commitment in the middle of the park was undeniable as they scrapped their way to victory.
Crewe, on the other hand, while creating chances looked certain to be fighting against the drop from League One until the final game.
Port Vale, cut adrift from the bottom of the table, are more or less certain of playing League Two football next season but they started the game in a high tempo and pushed Crewe back into their half.
Harsley and Chris Herd forced keeper Ben Williams to save early long-range efforts, but Harsley wasted a good chance to apply more pressure on the home goal when he cracked his free-kick straight at the Crewe wall.
Crewe took until the 18th minute to mount an attack, but when they did Tom Pope flicked a header on to the top of the woodwork from Dean Morgan's cross.
Morgan also showed his intent to go for goal as the half closed with two efforts which went narrowly wide.
Port Vale keeper Joe Anyon came to his side's rescue with a great save seven minutes into the second half after tipping Pope's 25-yard volley onto the roof of the net.
George Pilkington made a last-ditch challenge to deny Pope as Crewe forced the issue.
But they were caught on the break when Herd's pass released Marc Richards, who was tripped by Danny O'Donnell.
Harsley slotted the 57th minute spot-kick into the bottom left-hand corner to give Vale a precious lead.
Rodgers made the three points safe with nine minutes left when he out-muscled O'Donnell and hooked the ball past Williams.