Pronay Halder, Narayan Das and Manvir Singh were out of action for the hosts as the trio were away on national team duties while the likes Ferran Corominas (Coro) and Edu Bedia were included in the starting XI along with Liston Colaco.
Mohun Bagan coach Sanjoy Sen started the match with a Gurjinder Kumar and Kingsley Obumneme pairing at the back. Aser Dipanda was deployed up-front with Yuta Kinowaki and Sony Norde manning the midfield. Liberian midfielder Ansumana Kromah missed the second match in a row for the Kolkata giants with visa related issues.
The ISL outfit started off with a goal in the second minute as a move down the left side saw Lanzarote in a promising position with only the goalkeeper to beat and the Spaniard did well to chip it over Shibinraj Kunniyil to disturb the Bagan net.
The combination on the left worked well for the Goan side with Mandar Rao Dessai pushed back to accommodate Brandon Fernandes on the wing with Coro and Lanzarote moving ahead in tandem while Liston manned the right flank.
One of Lanzarote's free-kicks was close to dropping into the back of the net before FC Goa extended their lead in the 21st minute. The move for the goal started from the right through Seriton Fernandes' pass to Mandar, who whipped in a low cross for Coro to convert first time into the bottom left corner.
Mohammed Ali and Sergio were brought on by Sergio Lobera in the second half in place of Bruno Pinheiro and Konsham Chinglensana Singh.
The I-League giants had calmed things down for a while as the play resumed though Coro constantly attempted getting past his marker while Kinowaki and Norde tried pulling the strings for the visitors.
It could have been 3-0 around the hour mark after a quick one-two between Brandon and Lanzarote resulted in the former's shot being thwarted away by Bagan substitute goalkeeper Soran Angamba.
FC Goa goalkeeper Laxmikant Kattimani probably had his first piece of goalmouth action when he had to punch away a corner taken by Norde before Liston missed a golden opportunity at the other end when the Goan failed to tap in an inch perfect cross by Lanzarote from the left.
Possibly the only clear chance for Bagan was when substitute Naro Hari Shrestha's first time volley from the top of the box from another substitute, Nikhil Kadam's delivery late into the game.
FC Goa will play their last pre-season friendly against Chennai City at the Bambolim Athletic Stadium before the ISL season 4 starts.