The South African side looked to be heading to victory in the pre-season fixture when Alcardo van Graan’s cheeky flicked goal three minutes from time put the home team ahead.
But United hit back almost straight away, when Marnick Vermijl’s low cross was turned in by Bebe from close range.
It was perhaps harsh on Ajax Cape Town, who had looked the better of the two sides in the closing stages of the match.
There were positives for United though, including a bright first start for summer signing Shinji Kagawa.
It was a largely uneventful game, which did not spark to life until the final 10 minutes.
United looked keen to play the first half at a quick pace, but a disciplined Ajax Cape Town defence made it difficult for the visitors to break through.
Indeed, it was Ajax Cape Town who had the first notable opportunity of the game, when Khama Billiat dragged his shot wide of the goal on his weaker foot.
United striker Javier Hernandez came closest to opening the scoring in the first period.
Young defender Scott Wootton attacked down the right and delivered a perfect cross for the Mexican, but his header was expertly stopped by former Liverpool goalkeeper Sander Westerveld.
Tafadzwa Paul Rusike nearly broke the deadlock just before half-time, when his viciously hit shot shaved the United cross bar on his way over into the crowd.
The second half largely played out the same way as the first, broken up by a number of changes from both sides.
As United’s young defence began to tire, Ajax Cape Town’s substitutions reinvigorated the team.
Alcardo van Graan’s clever finish in the 87th minute was worthy of winning a game, and it looked to heading that way.
A poor corner from Khama Billiat found it’s way to van Graan, who, with his back to goal, back heeled the ball to loop over Ben Amos into the United net.
That sparked more urgency from the Premier League outfit, as first Ryan Tunnicliffe and then promising new signing Nick Powell went close to getting the equaliser.
They drew level two minutes into added time, as Vermeij’s drilled ball across goal fell to Bebe, who controlled before volleying into the Ajax Cape Town goal.
United continue their pre-season tour by travelling to China next, where they play Shanghai Shenhua on Wednesday.