The temporary shutdown wiped 20% off exports in the sector and contributed to a 4% decline in all Scottish export sales in the last three months of 2013 compared with the previous quarter, Scotland's chief statistician said.
Despite the quarterly drop, annual figures were more encouraging with a 1.9% year-on-year increase in total exports, the fastest since 2008.
Finance Secretary John Swinney said the annual rise, coming on the back of GDP growth and rising employment, is further evidence of "the continued recovery of Scotland's economy".
Exports of food and drink products were down 5.5% during the last quarter, but the sector saw continued export growth of 2.4% over the year.
Mr Swinney said: "The annual growth in manufactured exports, the fastest seen since 2008, is welcome news for Scottish businesses and the wider Scottish economy.
"This comes in the same month employment levels in Scotland surpassed pre-recession levels, reaching a record high, and the latest GDP figures show sustained economic growth over the last seven quarters, demonstrating the continued recovery of Scotland's economy.
"While this annual growth in exports is welcome news, the 4% fall in exports over the most recent quarter shows the continued challenges facing Scotland in the global marketplace, where the muted recovery in the euro area and volatility in emerging economies continues to have an impact across a range of export areas.
"As we saw in the economic growth figures for this quarter, the temporary shutdown at the Grangemouth petrochemical complex has had a one-off impact on production and sales of refined petroleum, chemicals and pharmaceutical products. Given the sector accounts for almost a quarter of exports this fall has had a significant impact on the overall figures, however we expect these figures to bounce back in future results.
"On food and drink, while there has been a fall in exports in the last quarter this comes against a backdrop of continual growth, which saw exports reach one of the highest levels on record in the first quarter of 2013.
"The Scottish Government is determined to do more to support export businesses, and that is why we are working with Scottish Development International, Scottish Enterprise and Highlands and Islands Enterprise to help companies reach new markets.
"Encouraging exports and strengthening Scotland's manufacturing base is a key part of our vision to improve the country's economic performance and to create new jobs.
"With the full powers of independence we would be able to use the full range of economic levers at our disposal to realise our ambition of creating a wealthier and fairer nation."
Grangemouth owners Ineos threatened to close the petrochemical site in October with the loss of over 800 jobs unless workers accepted changes to pay, pensions and terms and conditions. The Unite union accepted the changes following a prolonged dispute and shutdown.
Scotland's chief statistician said: "The Scottish Index of Manufactured Exports for the period October to December 2013 registered a real-terms fall of 4% from the previous three months.
"The largest contributors to the quarterly contractions were the refined petroleum, chemical and pharmaceutical products sector and the food and drink sector, which together account for more than half of international manufactured exports from Scotland.
The volume of refined petroleum, chemical and pharmaceutical products exports contracted 20% from the previous quarter. This largely reflects a reduction in export volumes during the temporary closure of the Grangemouth refinery and petrochemical complex in October 2013."
Last week, the Grangemouth shutdown was also blamed for a slowdown in the overall Scottish economy at the end of 2013, with GDP growth of 0.2% compared with growth of 0.7% in the UK.