Roberto Mancini's high-fliers looked set for all three points at the Britannia Stadium thanks to a marvellous goal from Micah Richards in the 81st minute.
But Stoke refused to lie down and Etherington took advantage of a clever back-heel from Tuncay to ensure his side got a share of the spoils.
City found themselves under pressure for long spells in the first half and must have been delighted to go in at the break on level terms.
Stoke showed their credentials as early as the fifth minute when a long throw from Rory Delap was flicked on by Ryan Shawcross.
Jermaine Pennant got on the end of it, clearing the bar with his effort before Delap caused further confusion in the City penalty area.
Ricardo Fuller found himself clear following a long throw, only to see his shot blocked by Vincent Kompany.
Etherington then took advantage of some defensive hesitancy to fire in a shot City goalkeeper Joe Hart got a hand to before the ball was scrambled away.
The home side should have taken the lead in the 16th minute when Fuller and Kenwyne Jones played a neat one-two.
Fuller was released in the area but failed to test Hart, steering his effort wide of the post.
City were again forced on the back foot in the 22nd minute when Robert Huth cleared the bar from a good position.
The visitors launched a quick counter-attack in the 31st minute when David Silva released Carlos Tevez.
The striker found James Milner but the move broke down following a timely challenge by Andy Wilkinson.
Back came Stoke and Fuller got goal-side of Kolo Toure only to send his shot into the arms of Hart.
Play switched down the other end and Aleksandar Kolarov tested goalkeeper Asmir Begovic from distance in the 36th minute.
Stoke were nearly undone in the 42nd minute following a mistake by Danny Collins. He played a casual back pass to Begovic, unaware Tevez was lurking on the edge of the area.
Begovic came to the rescue, racing out of his goal to divert the ball to safety.
Mario Balotelli had started the half with purpose for City and showed good strength and pace to rattle in a shot in the 52nd minute that went narrowly wide.
Stoke hit back and Fuller got on the end a ball from Etherington two minutes later and skipped into the area but sent a soft shot into Hart's body.
Then Etherington's miscued effort was met at the back post by Shawcross, However the defender was off balance and headed over the bar.
Fuller was finding it hard going in the second half and replaced by Jon Walters in the 75th minute.
His arrival gave Stoke a bit of impetus and Jones saw his effort cleared off the line by Milner before Tuncay fired the rebound over the bar.
City, however, made the breakthrough in the 81st minute with a marvellous piece of skill from the recalled Richards.
He latched on to a ball from Milner, sold a dummy to Collins before rifling a shot into the corner from the edge of the area.
Stoke, though, secured a point in stoppage time through Etherington, who got on the end of a clever back heel from substitute Tuncay. Although Hart got a hand to the ball he could not prevent it going into the net.