Cellphone users were able to make calls but not send SMS messages in an apparent effort to prevent candidates transmitting campaign messages on polling day.
EU chief observer Thijs Berman wrote to election officials to warn the move would "seriously handicap" the work of candidates' agents, who monitor polling stations, and could even affect their safety.
If the suspension lasted until after polls closed, he warned, "the very valuable work of the thousands of observers would also be severely affected".
"It's a risk to their security and also a risk to the transparency of the vote."
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The 2009 vote in which President Hamid Karzai was re-elected was marred by massive fraud.
A repeat would undermine the credibility of his successor as he leads Afghanistan at a testing time, with NATO forces pulling out and Afghan troops fighting a still-resilient Taliban insurgency.
An official at the Afghanistan Telecom Regulatory Authority said suspension came after an Election Complaints Commission (ECC) complaint saying around a million text messages had been sent after campaigning had officially closed.
Afghans voted today for a successor to Karzai, who has led the country since the 2001 fall of the Taliban, in an election seen as a major test of the troubled country's stability after a 13-year US-led military intervention.