The East African derby, played at the Stade El Barid, carried huge significance for Uganda, who were seeking their first win of the tournament to keep qualification hopes alive.
With the match deadlocked at 1-1 heading into the final moments, the Cranes were handed a golden opportunity to claim all three points when James Bogere was fouled inside the penalty area in the 90th minute.
Playmaker Okello, 25, stepped forward to take responsibility, but his effort sailed over the crossbar, leaving Uganda to settle for a single point in what was effectively a must-win fixture.
According Sportpesablog, Onyango insisted the team remains united and warned against singling out Okello for criticism.
"The team is behind him regardless of what has happened," Onyango said.
"Maybe he will be our match winner against Nigeria, you never know. We need to protect him and keep him strong because that's the game of football. He missed the opportunity to win it for us, but they also had opportunities and could have won it."
The veteran goalkeeper, who came out of international retirement to lead the Cranes in Morocco, stressed that the experience should serve as a valuable lesson for the young midfielder.
"That's football. We believe he will learn from it and come back stronger because he is still a young man," Onyango added.
The result leaves Uganda bottom of Group C with just one point from two matches, following their opening 3-1 defeat to Tunisia.
To keep their hopes of reaching the knockout stages alive, the Cranes now face a daunting final group match against Nigeria on Tuesday.
The Super Eagles have already secured qualification after victories over Tunisia and Tanzania, but Onyango believes Uganda can still produce a historic upset.
"A lot needs to be done, more hard work is needed because we are going to play a very good team," he said.
"They have quality individually and as a group, but in every game you get moments. It's how you take them, and we believe we can cause an upset."
For automatic qualification, Uganda must beat Nigeria and hope Tanzania draw or defeat Tunisia while also overcoming a significant goal difference gap.
A win would also give the Cranes a chance of progressing as one of the best third-placed teams, depending on results elsewhere.