The announcement follows Adam Crozier, former chief executive of Royal Mail, joining ITV as its chief executive on 26 April. He is currently working with strategy firm LEK Consulting on a comprehensive review of the business.
Howell will step down from the board on 1 June and as managing director of ITV Brand and Commercial at the end of July.
As managing director of brand and commercial at ITV Howell held the most senior commercial role at the broadcaster and media agencies suggest it was always unlikely that he would retain his role under the new regime.
Crozier said: "Under Rupert's leadership the commercial team has made significant progress in adapting to the challenges of the new media marketplace. We will continue on that journey, working in close partnership with our advertisers as we transform ITV's business over the next three to five years."
Howell is an advertising veteran with more than 25 years of experience and was the co-founder of ad agency HHCL and led the EMEA division of Interpublic ad network McCann Erickson before he joined ITV in 2007.
One TV industry insider suggested the move could help the UK's largest commercial broadcaster to adapt to a changing market.
He said: "ITV's biggest issue is that they have been a one trick pony. They have been selling TV in the same way for 30 years and need to find a different model.
"The TV ad market has previously grown because it has introduced different advertising categories, but it hasn't been able to do that more recently. ITV needs to use ad space in a way that's more congruent but I think they realise this. They've got to start making more of their assets."
However, others suggested Howell's departure will not be the start of significant changes in the sales team because there it operates a tried and tested model.
One less friendly agency trader suggested some senior management at ITV have grown tired of Howell's "endless self-promotion" and while he has undisputed strong links with clients he does not believe his departure now will have an impact on the broadcaster's newly invigorated offering.
Meanwhile, the restrictions of the recently maintained Contract Rights Renewal (CRR) mean ITV's sales operations are in many ways dictated by its obligations. The broadcaster has to continue to sell its air time regionally for example, which Carl Nawagamuwa, account director of Mediaedge:cia, said is "completely irrelevant" for some advertisers and would benefit from being streamlined if future legislation allows.
Richard Oliver, managing partner, Universal McCann
"It's not a complete surprise that Crozier has decided they can't work together after Howell had put himself up for the top job. I'm not sure how many more imminent changes there can be in the sales team. The people there have done a great job; they're very well connected and respected. The physical business requires a sales team of a certain size."
Carl Nawagamuwa, account director, Mediaedge:CIA
"The departure of Howell will allow Adam Crozier to do what he wants with the commercial business. You expect a new chief executive to put his own stamp on things and there are so many people in their sales team there could be losses at a middle management level. If the regional teams were allowed to merge a national team might be able to look more closely at how they can maximise revenue."
Mark Jarvis, founding partner at the7stars
"I think that Rupert changed a few things within ITV sales and was very good at being an account man and made ITV more approachable from an advertiser perspective.
"However, whether Rupert's departure will affect ITV I doubt. It still has a very strong sales proposition led by Gary Digby, who is more than capable of running a sales team and bridging that gap."
Chris Wright, head of broadcast at Initiative
"There's no doubt that Rupert made ITV more customer-centric commercially, but there are always going to be casualties with the change in top level management. Hiring Rupert was a good step forward for ITV and I'm pleased to say that it seems to be investing more in its customer facing teams."