After Friday's first leg clash ended 0-0, the two teams couldn't be separated after regulation time with Botswana advancing through on penalties to break Banyana Banyana hearts.
Ellis, who couldn't hide her disappointment described the result as a disaster, calling it their lowest low.
"When you have so many chances but can't score it's disappointing, Ellis said. "We could have been 4-nil up at half-time, it's really a disaster and we're all very disappointed.
"We never took anything for granted, we really worked hard in training at everything, but we couldn't put even one into the net and that's disappointing.
"It's a problem that we have in local soccer as a whole. We haven't won many games this year but gave a good account of ourselves in the World Cup but this is definitely a dull moment for us as a team."
Compiled by Baden Gillion