(Read more: Pimco CEO El-Erian resigns)
El-Erian, CEO and co-chief investment officer, will leave Pimco in March. Gross will become the lone CIO.
"I'm disappointed. We're disappointed. When he came back [to Pimco] six years ago ... we thought he would be my successor and would be in place for 10 to 15 years. That's not going to be the case," Gross said on "Street Signs."
"We're disappointed that he won't be with Pimco; that he didn't, you know, continue in the successor role for me as chief investment officer," Gross said. "But that is the way it is and we're going to move forward."
(Read more: Pimco's problem: Who can succeed the 'Bond King'?)
Though published reports suggested there was a clash of strategy and some tense moments between the two executives, Gross said that had nothing to do with El-Erian's decision to leave Pimco. Gross noted the two are personal friends, who live nearby and enjoy chatting about professional football.
"I hired him twice, so that couldn't have happened unless we got along," Gross said. "There's no clash of personalities here. we got along real well."
Gross said he doesn't know where El-Erian will land, except to point out that he doesn't plan to take another job in the financial industry. Nevertheless, Gross thinks El-Erian will be tapped for a role "in elevated circles of influence."
Meantime, Gross doesn't think El-Erian's decision was related to fund performance either. Though bonds have taken a hit in the wake of the Federal Reserve's bond-buying program, Gross noted Pimco's total return fund outperformed the market last year, even despite outflows.
"Like an architect, Mohamed basically, you know, put in place a structure that will carry us forward over the next five and 10 years, and perhaps like an architect, he is moving on to another house."