Pyrgos is one of five changes to the starting lineup in the squad announced by head coach Andy Robinson on Wednesday.
Max Evans returns at outside centre in the stadium where he won his first cap four years ago in place of Nick De Luca who is relegated to the bench.
Pyrgos starts ahead of Mike Blair while Scott Lawson will begin his first international since August 2011 at hooker rather than Ross Ford.
Alastair Kellock has been preferred to Jim Hamilton at lock and Alasdair Strokosch will play at blindside flanker after recovering from the calf injury which kept him out of the match against the Springboks.
Scotland lost their opening November internationals against world champions New Zealand and the Springboks.
"We will not be among the top eight seeds for the 2015 Rugby World Cup draw, so this weekend I'm looking at giving a number of players an opportunity to put their hand up for selection for next year," Robinson said in a statement.
"This weekend we have to put together an 80 minutes performance and build on the positive parts of our games that we showed in the last 30 minutes against South Africa and the second half against New Zealand."
Tonga have made a solitary change with Hale T-Pole called up to start.
The Northland flanker replaces Leicester's Steve Mafi in the back-row following the 22-13 win over the United States at Colwyn Bay last weekend.
Coach Mana Otai has retained former Glasgow Warriors number eight Viliami Ma'afu in the line-up.
Ma'afu joined the Warriors in February, but left in September, citing personal reasons and is currently looking for a new club.
London Irish prop Halani Aulika, Newcastle Falcons centre Suka Hufanga and Connacht wing Fetu'u Vainikolo are also in the team.
Mafi is among the replacements, along with Llanelli lock Sione Timani joins Mafi among the replacements as Tonga seek the second win of their European tour.
Scotland: 15-Stuart Hogg, 14-Sean Lamont, 13-Max Evans, 12-Matt Scott, 11-Tim Visser, 10-Greig Laidlaw, 9-Henry Pyrgos, 8-David Denton, 7-Kelly Brown, 6-Alasdair Strokosch, 5-Alastair Kellock, 4-Richie Gray, 3-Euan Murray, 2-Scott Lawson, 1-Ryan Grant.
Replacements: 16-Dougie Hall, 17-Kyle Traynor, 18-Geoff Cross, 19-Grant Gilchrist, 20-John Barclay, 21-Rory Lawson, 22-Tom Heathcote, 23-Nick De Luca.
Tonga: V Lilo, F Vainikolo, S Hufanga, S Piukala, W Helu, F Apikotoa, T Moa; A Taumalolo, E Taione, H Aulika, J Tu'ineau, T Lokotui, H T-Pole, N Latu (captain), V Ma'afu.
Replacements: I Ma'asi, T Mailau, K Sakalia, S Mafi, S Timani, V 'longi, E Paea, A Fatafehi.