Mr Ross was informed by text on Wednesday morning around 8:40am that Mr Duguid, who he had met with on Monday, had tested positive for Covid-19.
The party leader was already in the Scottish Parliament building when notified, but later returned to an Edinburgh hotel where he is staying.
Mr Ross will take a test “as soon as possible”, the Scottish Conservatives said.
The Scotland Office confirmed Mr Duguid had taken a test as a precaution, but was not experiencing any symptoms and is said to be well.
The self-isolation comes a day after the Tory leader was in the Holyrood chamber responding to Nicola Sturgeon’s announcement around the next stage of Covid-19 restrictions easing.
In a statement, the party said both Holyrood officials were informed Mr Ross was a close contact of a Covid-19 positive person while he remained in his office before deciding to return to his hotel.
The hotel was also told he would be self-isolating.
Both he and Mr Duguid were together on Monday in Peterhead, speaking to local fishermen about the impacts of the pandemic.
A spokeswoman for the Scotland Office said: “Minister Duguid is self-isolating after testing positive for coronavirus.
“He took a test as a precaution at a local UK Government test centre. He has notified those he was in close contact with.”
Despite the test, Mr Duguid is said to not have had any contact with other ministers, including Scottish Secretary Alister Jack.
At least four MSPs and five members of Scottish Conservative staff have been instructed to take Covid-19 tests as soon as possible as a precaution, with two MSPs from another party also told they may want to take a test as a precaution.
Despite self isolation, Mr Ross is expected to appear at First Minister’s Questions virtually on Thursday, rather than handing the duties over to chief whip Stephen Kerr, who was designated as his replacement during the weekly session in the announcement of the Tory front bench.