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The England man, starting just his second game after recovering from a foot injury, converted after Leon Osman had been tripped in the area.
It was the least Everton deserved from a game that saw them create the better chances, but the joy of a last minute goal is tempered by the feeling this represented two points dropped in the quest for a top four place.
Roberto Martinez again opted to re-shuffle his starting line-up following an energy sapping festive period. Back came Tim Howard and Gareth Barry from suspension, while Steven Pienaar and Kevin Mirallas were promoted from the substitutes bench. There was also a first Premier League for youngster John Stones, a little under a year since his £3million move from Barnsley.
When the fixtures were announced last June and Everton were paired with Stoke on New Year’s Day, I had a vivid image in my head of how the match would pan out; It was going to be grim, cold, wet and windy.
Just as predicted, the game kicked off under gloomy skies, heavy rain and the familiar swirling wind whipping round this exposed stadium. This wasn't going to be pretty.
On the pitch, Everton dominated the early possession without really creating any genuine openings.
The early exchanges were littered with only half chances; Charlie Adam’s deflected effort that was easily saved by Howard, while at the other end James McCarthy’s shot was comfortably dealt with by Thomas Sorensen.
Then, almost out of nowhere, Everton very nearly took the lead when Mirallas cut inside and fired in an effort that thumped off the crossbar.
The Belgian was looking livelier than he had been in a long while and created another opportunity for Barkley a few minutes later, but his shot went over.
Everton by now were on top and were cursing their luck again when Mirallas curled in a free kick that smacked off the post while Romelu Lukaku headed a Seamus Coleman cross wide second later.
The half time whistle came at a poor time for the Blues as it stymied their momentum, so it was typical that Stoke scored with virtually their first chance of the second half.
John Stones was perhaps guilty of not getting enough on his headed clearance from Glenn Whelan’s cross, the ball falling to the feet of Liverpool loanee Oussama Assaidi, who blasted beyond Howard.
Echoes of three years ago, when Everton fell to a miserable 2-0 defeat at the Britannia Stadium on New Year’s Day, came flooding back as the weary players gamely tried to battle back into the game.
Steven Pienaar fired wide when well-placed while Lukaku saw an effort saved by substitute ‘keeper Jack Butland, who replaced Sorensen at half time. Stoke defender Erik Pieters was then at his best to block a Mirallas effort before deflecting Barkley’s shot wide.
Time was rapidly coming out and it looked like being another one of those days that we experienced on Boxing Day, when Everton huffed and puffed but failed to blow the Sunderland house down.
Thankfully Jermaine Pennant was clumsy in his attempt to tackle Osman in the area and tripped the midfielder, giving Baines the chance to secure a point at the death.
Given Everton were seconds away from defeat we have to be pleased with a draw from what remains a tough ground to go to, especially in the wet winter gloom.
However, if Everton are to pierce the top four then draws need to be converted into wins, with games like today a key example of that.
The busy festive period was undoubtedly a factor, with Martinez doing his best to rotate the side. But with the January window now open, today’s game again emphasised the need to bolster the squad with experienced recruits, in order to help the club emerge from these energy sapping next few weeks with their top four hopes still intact.
Howard 7 Coleman 6 Stones 7 Alcaraz 7 Baines 7 Pienaar 7 (Osman 7) McCarthy 7 (Jelavic 6) Mirallas 8 Barry 7 Barkley 8 Lukaku 6 (Naismith 6)