The Dons eventually took the lead on 40 minutes as Gary Dempsey slotted past Howard from a Stephen Crawford cutback.
Everton made three changes at the interval, the most telling being the introduction of Mikel Arteta.
The Spaniard shone after his introduction and it was from his left wing cross that Beattie levelled matters on 53 minutes.
After being fed down the left by Phil Neville, on for Alessandro Pistone, Arteta clipped in a cross that Beattie got the deftest of touches on to steer a header past Langfield in the Aberdeen goal.
Everton made four more changes just after the hour as Howard was replaced by Richard Wright, Nuno Valente made way for Gary Naysmith and Stubbs came on for Yobo and Anichebe for Beattie.
But it was
Jamie Smith, who looked the most likely to score in the first half, was played through on the edge of the area and hammered a shot past the Wright's despairing dive.
But, as the game was approaching the final whistle, Ateta took control once more and freed Anichebe whose low cross was poked in from close range by Tim Cahill.
Arteta then released Neville and his low cross was drilled home on the half volley by Victor Anichebe who sealed another win for the Blues.
This was another good test for Everton against a decent SPL team that already has two league games under it's belt.
Next up is Athletic Bilbao at Goodison on Saturday for Howard Kendal's testimonial.