Presiding Officer Ken MacIntosh said the attack on the “sister parliament” was having an impact on business and MSPs contributions during the debate.
He also said that security has been tightened at Holyrood in light of the incident in London.
The move came after his deputy, Linda Fabiani, told MSPs the debate would carry on and it was “business as usual.”
Mr MacIntosh later intervened to halt proceedings.
“Members will be aware that there has been a series of incidents at Westminster and Westminster itself has been locked down because of security concerns.
“Now there is no wish to cause undue alarm here and security has been increased here but I’m also aware, and business managers and I have discussed this, that the fact that our sister Parliament has had a serious incident is affecting this particular debate and its affecting the contribution of members.
“So it is for that reason we are deciding to suspend.”
The debate and vote SNP Government demands that Westminster allow a second referendum to take place is now likely to be concluded at a later date.
“We will resume this debate and we will be able to do so in a full and frank manner,” Mr Macintosh added