Yes, you can.
The Companion keyword only functions outside of the game. This means that if a card with Companion is in your deck, whether as a Commander or just any regular card, then the Companion part of the card doesn't do anything; it's just a normal creature. In the case of a Commander deck, it would just be a normal Legendary Creature which is therefore valid as your Commander.
702.138. Companion
702.138a Companion is a keyword ability that functions outside the game. It’s written as “Companion—[Condition].” Before the game begins, you may reveal one card you own from outside the game with a companion ability whose condition is fulfilled by your starting deck. (See rule 103.1b.) If you do, once during that game, you may play that card from outside the game.
- Commander
903.3. Each deck has a legendary creature card designated as its commander. This designation is not a characteristic of the object represented by the card; rather, it is an attribute of the card itself. The card retains this designation even when it changes zones.
Jegantha, the Wellspring is a legendary creature, therefore it can be your Commander.