The Scottish National Party held the Banff and Buchan seat vacated after former party leader Alex Salmond's decision to concentrate on Westminster politics.
And Labour has held the Strathkelvin and Bearsden constituency which had been the seat of former Scottish Executive minister Sam Galbraith, who has resigned from politics on health grounds.
The new Labour MSP Brian Fitzpatrick won by a majority of almost 8,000.
An independent candidate, Jean Turner, who was campaigning to save the local Stobhill hospital came in second, beating the Lib Dems and SNP into third and fourth place.
Former bank director Stewart Stevenson held onto the Banff and Buchan seat for the SNP with a majority of 8,500 votes over the Conservative candidate.
The SNP vote was slightly down on Alex Salmond's result two years ago, while the Tories increased their share.
Canon Kenyon Wright, one of the key architects of the Scottish Parliament, stood as a Liberal Democrat but was beaten into fourth place behind Labour.
In 1999, both Mr Salmond and Mr Galbraith polled more than 50% of the votes in their respective constituencies.
All the parties campaigning in the by-elections consistently stressed the polls were more than mere side shows to the general election.
The departure of these two prominent politicians offered a chance for other parties to secure the vacant seats.
But it also set the respective candidates the significant challenge of succeeding MSPs who have been instrumental in their own parties' electoral success.
Voters made their choice on Thursday at the same time as they voted in the general election.