"The board wishes to record its thanks and recognition of the major achievements he has overseen," it said.
"It also recognises the substantial impact that Covid-19 has had on Synlait and the difficult challenge this would present to any management team."
Clement will continue in his role until the end of April.
Penno will take over from May 1.
Synlait chair Graeme Milne said Clement had been "an authentic and transformational leader".
"He has successfully repositioned Synlait's purpose, ambition, and strategy to make us a more diversified and sustainable company," he said.
Clement said the board had thanked Clement "for his energy and dedication to Synlait" during his time at the company.
In the statement, Clement said: "It has been an intensive period of change and growth and I am proud of our achievements.
"Synlait has an amazing team that is making a positive and sustainable impact in the areas we operate."
Late last month, Synlait - which his a2 Milk's sole infant formula supplier - said its half-year profit slumped by 76 per cent to $6.4m, driven by Covid-19 disruption, and said it expected to be "broadly breakeven" in the full year.
The full-year outlook has worsened since last December when the company said it expected the 2021 profit to be half that of the previous year's $75.2m.
In early March, the company withdrew that December guidance due to uncertainty and volatility within its business.
Milne said at the time that it had been a challenging first half, "and we continue to find ourselves in a period of significant uncertainty and volatility as Synlait faces into several headwinds".
Synlait is 39 per cent owned by China's Bright Dairy and just under 20 per cent by a2 Milk.
In today's statement, Synlait listed Clement's achievements as being:
• Refreshed strategy and new company purpose: Doing Milk Differently For A Healthier World.
• Maintained growth momentum towards $2 billion revenue target with more than $500 million of top-line growth delivered, achieving more than $1 billion in revenue for first time in FY19 and delivering a record NPAT result of $82.2 million.
• Issued $180 million of unsecured, subordinated, fixed-rate bonds to the NZX Debt Market.
• Successfully completed a $200 million equity raising.
• Purchased Dairyworks Limited, extending Synlait's consumer foods strategy.
• Synlait Pokeno and Dry Store 4 projects completed on time and budget.
• Signed a manufacturing supply agreement with an established, global category leader.
• Comprehensive sustainability strategy and roadmap developed to deliver 2028 targets.
Shares in Synlait last traded on Friday at $3.50, having dropped by 51.6 per cent over tge last 12 months.
