It comes amid tense relationships between Canberra and Honiara after the Solomons Island signed a security pact with China.
A spokesman for Senator Payne confirmed the meeting occurred as Mr Manele travelled through Brisbane on Friday.
Trade Minister Dan Tehan said he was told it had been a "very productive conversation".
"Talking about how we respect the sovereignty of the Solomon Islands but how we are very concerned about the security agreement with China," Mr Tehan told the ABC on Saturday.
Senator Payne's spokesman said the pair had agreed Australia was the Solomon Islands' security partner of choice and was reassured the Pacific nation would not house a foreign military base.
Mr Tehan said the pair had also discussed how the Morrison government needed to keep working at the relationship.
Prime Minister Scott Morrison has warned any construction of a Chinese military base in the Solomon Islands would be a "red line".
But he has not detailed what the consequences would be if the line was crossed.
Mr Tehan said the point being made was that no one saw a Chinese base in the Solomon Islands as in the interests for the region.
"What we want to do is to be making sure that we're presenting a very strong case as to why it is incredibly important that we don't see militarisation of the Pacific Islands," Mr Tehan said.
Labor leader Anthony Albanese said it was good Senator Payne and Mr Manele had met.
"It's about time," he said.
Labor has attacked the Morrison government's handling of ties with the Solomon Islands, with deputy leader Richard Marles saying on Friday that repairing the relationship with the nation would be a priority for his party.
"It's really important, obviously, that Australia presents itself as wanting to help the people of the Pacific in the challenges that they face," he said.
Prime Minister Manasseh Sogavare told the Solomon Islands parliament this week the country was being treated like kindergarten students "walking around with Colt 45s in our hands" who needed to be supervised.