Argentina squeezed into the World Cup last 16 after Marcos Rojo's fine late volley gave them a 2-1 win over Nigeria in St Petersburg.
With Nigeria heading through in Group D with four minutes remaining, the Manchester United defender popped up to convert Mercado's cross and send Jorge Sampaoli's side through in dramatic fashion.
Needing a win to stand a chance of qualifying, Argentina went ahead through Messi (14), turning home from 10 yards at a slight angle after Ever Banega superbly found him from deep.
Messi then hit the post with a free-kick, but Nigeria was allowed a path into the game as Victor Moses slotted home a penalty (51) from Javier Mascherano's tug on Leon Balogun from a corner.
But Argentina won it, meaning they'll play France in Kazan on Saturday, while Croatia will play Denmark on Sunday.
In their third and final group game, Sampaoli went for five changes and 4-4-2, his third different formation of the World Cup, but it worked early on.
Banega, one of the incoming midfielders, played a fine ball from deep over the Nigeria defence for Messi, whose touch was superb before finishing past Francis Uzoho with his weaker right foot.
Messi's fine through ball gave Gonzalo Higuain the chance to double their lead before the half-hour mark, but the Juventus striker couldn't dink the ball over the out-rushing Uzoho.
Messi, who had been criticised in Argentina's first two games for looking out of sorts, was in the mood in St Petersburg, hitting the post with a 20-yard free-kick, though Uzoho can be credited again for getting the slightest touch on his effort.
Early in a dramatic second half, Mascherano first gave away a needless corner before grappling with Balogun from the resulting cross, with Turkish referee Cuneyt Cakir going to VAR before awarding the spot-kick.
Victor Moses duly converted, meaning Nigeria were through as it stood.
Odion Ighalo then missed a clear chance to put Nigeria ahead as the ball dropped kindly to him 10 yards out, while at the other end Higuain blazed over unmarked in the box from Rojo's centre.
But Argentina got their vital winner shortly after, as Rojo met Gabriel Mercado's cross from the right superbly, slamming low past Uzoho from 12 yards and sparking jubilant scenes on and off the pitch.
Argentina will now play France in Kazan on Saturday, having finished second in Group D.
Winners Croatia face Denmark on Sunday.